diff --git a/bin/create_interactive_table.py b/bin/create_interactive_table.py index 17711c23..569bdd2f 100644 --- a/bin/create_interactive_table.py +++ b/bin/create_interactive_table.py @@ -33,7 +33,10 @@ def generate_table( output_path: str, ) -> None: df = pd.read_csv(tsv_path, sep="\t").assign(Expand=lambda df: "").fillna("") - df = df[df["To keep"]].loc[:, COLUMNS].reindex(columns=COLUMNS) + if "To keep" in df.columns: + df["To keep"] = df["To keep"].replace("", True) + df = df.query("`To keep`") + df = df.loc[:, COLUMNS].reindex(columns=COLUMNS) table = df.to_html(border=0, table_id="dataframe", classes=["display", "nowrap"], index=False) with open(template_path) as template_file: diff --git a/bin/extract_all_tools.sh b/bin/extract_all_tools.sh index 1dc96028..f4e03534 100644 --- a/bin/extract_all_tools.sh +++ b/bin/extract_all_tools.sh @@ -5,4 +5,9 @@ mkdir -p 'results/' python bin/extract_galaxy_tools.py \ extractools \ --api $GITHUB_API_KEY \ - --all_tools 'results/all_tools.tsv' \ No newline at end of file + --all_tools 'results/all_tools.tsv' + +python bin/create_interactive_table.py \ + --table "results/all_tools.tsv" \ + --template "data/interactive_table_template.html" \ + --output "results/index.html" \ No newline at end of file diff --git a/bin/get_community_tools.sh b/bin/get_community_tools.sh new file mode 100644 index 00000000..b2f9b4fe --- /dev/null +++ b/bin/get_community_tools.sh @@ -0,0 +1,39 @@ +#!/usr/bin/env bash + + +for com_data_fp in data/* ; do + if [[ -d "$com_data_fp" && ! -L "$com_data_fp" ]]; then + community=`basename "$com_data_fp"` + + echo "$community"; + + if [[ "$community" == *"microgalaxy"* ]]; then + curl \ + -L \ + "https://docs.google.com/spreadsheets/d/1Nq_g-CPc8t_eC4M1NAS9XFJDflA7yE3b9hfSg3zu9L4/export?format=tsv&gid=1533244711" \ + -o "data/$community/tools_to_keep" + + curl \ + -L \ + "https://docs.google.com/spreadsheets/d/1Nq_g-CPc8t_eC4M1NAS9XFJDflA7yE3b9hfSg3zu9L4/export?format=tsv&gid=672552331" \ + -o "data/$community/tools_to_exclude" + fi; + + + mkdir -p "results/$community" + + python bin/extract_galaxy_tools.py \ + filtertools \ + --tools "results/all_tools.tsv" \ + --filtered_tools "results/$community/tools.tsv" \ + --categories "data/$community/categories" \ + --exclude "data/$community/tools_to_exclude" \ + --keep "data/$community/tools_to_keep" + + python bin/create_interactive_table.py \ + --table "results/$community/tools.tsv" \ + --template "data/interactive_table_template.html" \ + --output "results/$community/index.html" + + fi; +done diff --git a/bin/get_microgalaxy_tools.sh b/bin/get_microgalaxy_tools.sh deleted file mode 100644 index b8684d5b..00000000 --- a/bin/get_microgalaxy_tools.sh +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env bash - -curl \ - -L \ - "https://docs.google.com/spreadsheets/d/1Nq_g-CPc8t_eC4M1NAS9XFJDflA7yE3b9hfSg3zu9L4/export?format=tsv&gid=1533244711" \ - -o "data/microgalaxy/tools_to_keep" - -curl \ - -L \ - "https://docs.google.com/spreadsheets/d/1Nq_g-CPc8t_eC4M1NAS9XFJDflA7yE3b9hfSg3zu9L4/export?format=tsv&gid=672552331" \ - -o "data/microgalaxy/tools_to_exclude" - -mkdir -p 'results/microgalaxy' - -python bin/extract_galaxy_tools.py \ - filtertools \ - --tools 'results/all_tools.tsv' \ - --filtered_tools 'results/microgalaxy/tools.tsv' \ - --categories "data/microgalaxy/categories" \ - --exclude "data/microgalaxy/tools_to_exclude" \ - --keep "data/microgalaxy/tools_to_keep" - -python bin/create_interactive_table.py \ - --table 'results/microgalaxy/tools.tsv' \ - --template 'data/interactive_table_template.html' \ - --output 'results/microgalaxy/index.html' diff --git a/data/datatable_template.html b/data/datatable_template.html deleted file mode 100644 index 6e03634a..00000000 --- a/data/datatable_template.html +++ /dev/null @@ -1,58 +0,0 @@ - - - - - - - - - - - - - - - - - - - - -
- -COMMUNITY_TABLE - -
\ No newline at end of file diff --git a/data/interactive_table_template.html b/data/interactive_table_template.html index 6e03634a..80008750 100644 --- a/data/interactive_table_template.html +++ b/data/interactive_table_template.html @@ -23,7 +23,7 @@ background-color: #00FFFF; color: #000000; min-width: 400px; - } + } + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ExpandGalaxy wrapper idGalaxy wrapper versionConda versionConda idStatusbio.tool idbio.tool nameEDAM operationEDAM topicDescriptionbio.tool descriptionStatusSourceToolShed categoriesToolShed idGalaxy wrapper ownerGalaxy wrapper source
2d_auto_threshold0.0.5scikit-imageTo updateAutomatic thresholdingTo updatehttps://github.com/bmcvImaging2d_auto_thresholdimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/
2d_feature_extraction0.1.1pandasTo update2D feature extractionTo updatehttps://github.com/bmcvImaging2d_feature_extractionimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/
2d_filter_segmentation_by_features0.0.1scikit-imageTo updatefilter segmentation by rulesTo updatehttps://github.com/bmcvImaging2d_filter_segmentation_by_featuresimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/
2d_histogram_equalization0.0.1scikit-imageTo update2d histogram equalizationTo updatehttps://github.com/bmcvImaging2d_histogram_equalizationimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/
2d_simple_filter0.0.3scikit-imageTo update2d simple filterTo updatehttps://github.com/bmcvImaging2d_simple_filterimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/
2d_split_binaryimage_by_watershed0.0.1scikit-imageTo updatesplit object by watershedTo updatehttps://github.com/bmcvImaging2d_split_binaryimage_by_watershedimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_split_binaryimage_by_watershed/
3d_tensor_feature_dimension_reduction0.0.1numpyTo updateDimensionality reduction for features (channels) of 3D tensor data using UMAPTo updatehttps://github.com/BMCV/galaxy-image-analysisImaging3d_tensor_feature_dimension_reductionimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/
anisotropic_diffusion0.2scikit-imageTo updateAnisotropic image diffusionTo updatehttps://github.com/bmcvImaginganisotropic_diffusionimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/
bfconvert6.7.0+galaxy16.7.0bftoolsTo updateConvert imageTo updatehttps://github.com/bmcvImaging, Convert Formatsbfconvertimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/
binary2labelimage0.4scikit-imageTo updateBinary 2 label imageTo updatehttps://github.com/bmcvImagingbinary2labelimageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/
binaryimage2points0.1numpyTo updateBinary Image to PointsTo updatehttps://github.com/bmcvImagingbinaryimage2pointsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/
color-deconvolution0.8scikit-imageTo updateColor-deconvolution methodsTo updatehttps://github.com/bmcvImagingcolor_deconvolutionimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/
concat_channels0.2scikit-imageTo updateConcatenate imagesTo updatehttps://github.com/bmcvImagingconcat_channelsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/
coordinates_of_roi0.0.4scikit-imageTo updateCoordinates of ROITo updatehttps://github.com/bmcvImagingcoordinates_of_roiimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/
count_objects0.0.5scikit-imageTo updateCount ObjectsTo updatehttps://github.com/bmcvImagingcount_objectsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/
curve_fitting0.0.3numpyTo updatePolynomial curve fitting to data pointsTo updatehttps://github.com/BMCV/galaxy-image-analysisImagingcurve_fittingimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/
detection_viz0.3scikit-imageTo updateDetection VisualizationTo updatehttps://github.com/bmcvImagingdetection_vizimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/
image_info0.26.7.0bftoolsTo updateExtracts image metadataTo updatehttps://github.com/bmcvImagingimage_infoimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/
image_registration_affine0.0.3scikit-imageTo updateIntensity-based Image RegistrationTo updatehttps://github.com/bmcvImagingimage_registration_affineimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/
imagecoordinates_flipaxis0.1pandasTo updateFlip coordinate axesTo updatehttps://github.com/bmcvImagingimagecoordinates_flipaxisimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/
labelimage2points0.2scikit-imageTo updateLabel Image to PointsTo updatehttps://github.com/bmcvImaginglabelimage2pointsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/
landmark_registration0.1.0scikit-imageTo updateLandmark RegistrationTo updatehttps://github.com/bmcvImaginglandmark_registrationimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/
mahotas-features0.7mahotasTo updateCompute image features using mahotas.To updatehttps://github.com/luispedro/mahotasImagingmahotas_featuresimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/
mergeneighboursinlabelimage0.3scikit-imageTo updateMerge Neighbours in Label ImageTo updatehttps://github.com/bmcvImagingmergeneighboursinlabelimageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage
overlay_images0.0.3scikit-imageTo updateOverlay two imagesTo updatehttps://github.com/BMCV/galaxy-image-analysisImagingoverlay_imagesimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/
permutate_axis0.2scikit-imageTo updatePermutates axesTo updatehttps://github.com/bmcvImagingpermutate_axisimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/
points2binaryimage0.2scikit-imageTo updatePoints to Binary ImageTo updatehttps://github.com/bmcvImagingpoints2binaryimageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/
points2labelimage0.3numpyTo updatePoints to label imageTo updatehttps://github.com/bmcvImagingpoints2labelimageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/
points_association_nn0.0.3numpyTo updateAssociation of points in consecutive framesTo updatehttps://github.com/BMCV/galaxy-image-analysisImagingpoints_association_nnimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/
projective_transformation0.1.2scikit-imageTo updateProjective transformationTo updatehttps://github.com/bmcvImagingprojective_transformationimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/
projective_transformation_points0.1.1scikit-imageTo updateProjective transformation of ROIs defined by pixel (point) coordinatesTo updatehttps://github.com/bmcvImagingprojective_transformation_pointsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/
scale_image0.4pillowTo updateScale imageTo updatehttps://github.com/bmcvImagingscale_imageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/
segmetrics1.4.0-11.4segmetricsTo updateImage segmentation and object detection performance measuresTo updatehttps://github.com/bmcvImagingsegmetricsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/
slice_image0.3scikit-imageTo updateSlice imageTo updatehttps://github.com/bmcvImagingslice_imageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/
split_labelmap0.2scikit-imageTo updateSplit LabelmapsTo updatehttps://github.com/bmcvImagingsplit_labelmapimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/
spot_detection_2d0.0.3imageioTo updateSpot detection in 2D image sequenceTo updatehttps://github.com/BMCV/galaxy-image-analysisImagingspot_detection_2dimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/
superdsm0.1.30.1.3superdsmUp-to-dateGlobally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy imagesUp-to-datehttps://github.com/bmcvImagingsuperdsmimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/
visceral-evaluatesegmentation0.52015.07.03visceral-evaluatesegmentationTo updateVisceral Project - Evaluate Segmentation ToolTo updatehttps://github.com/bmcvImagingvisceral_evaluatesegmentationimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation
wsi_extract_top_view0.2scikit-imageTo updateWSI Extract Top ViewTo updatehttps://github.com/bmcvImagingwsi_extract_top_viewimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/
cellprofilerTo updatecellProfiler wrapperTo updateImagingcellprofilerbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools
cellprofiler_v44.2.1To updatecellProfiler4 wrapperTo updateImagingcellprofiler4bgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools
graphicsmagick1.3.311.3.26graphicsmagickTo updateContains tools based on GraphicsMagickTo updatehttp://www.graphicsmagick.orgImaginggraphicsmagickbgrueninghttps://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/
imagej2To updateImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.To updatehttp://fiji.scImagingimagej2imgteamhttps://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2
spyboat0.1.2spyboatTo updateWavelet analysis for 3d-image stacksTo updatehttp://github.com/tensionhead/spyboatImaging, Graphicsspyboatiuchttps://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat
qupath_roi_splitter0.1.0+galaxy1geojsonTo updateSplit ROI coordinates of QuPath TMA annotation by cell typeTo updatehttps://github.com/npinter/ROIsplitterImagingqupath_roi_splittergalaxyphhttps://github.com/npinter/ROIsplitter
hyperstack_to_bleach_corrected_movie2023032820220414FijiTo updateGenerate blach corrected movie from hyperstackTo updateImaginghyperstack_to_bleach_corrected_movielldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie
incucyte_stack_and_upload_omero2023082420220414FijiTo updateCombine images to stack and upload to the omero serverTo updateImagingincucyte_stack_and_upload_omerolldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero
measure_gastruloids2022121620220414fijiTo updateGet the ROI coordinates around the gastruloids as well as measurements like Area, elongation indexTo updateImagingmeasure_gastruloidslldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids
omero_clean_rois_tables2023062320220414fijiTo updateRemove all ROIs and all tables on OMERO associated to an omero object and recursively up and downTo updateImagingomero_clean_rois_tableslldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables
omero_hyperstack_to_fluo_measurements_on_gastruloid2023080920220414fijiTo updateAnalyse Hyperstack on OMERO server to measure fluorescence levelsTo updateImagingomero_hyperstack_to_fluo_measurements_on_gastruloidlldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid
omero_hyperstack_to_gastruloid_measurements2023072820220414fijiTo updateAnalyse Hyperstack on OMERO server to segment gastruloid and compute measurementsTo updateImagingomero_hyperstack_to_gastruloid_measurementslldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements
upload_roi_and_measures_to_omero0.0.55.11.1omero-pyTo updateUpload the ROI coordinates and the measurements to the omero serverTo updateImagingupload_roi_and_measures_to_omerolldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero
+ +
\ No newline at end of file diff --git a/results/imaging/tools.tsv b/results/imaging/tools.tsv new file mode 100644 index 00000000..09690f00 --- /dev/null +++ b/results/imaging/tools.tsv @@ -0,0 +1,53 @@ +Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper version Conda id Conda version Reviewed To keep +2d_auto_threshold ip_threshold Automatic thresholding To update https://github.com/bmcv Imaging 2d_auto_threshold imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ 0.0.5 scikit-image False +2d_feature_extraction ip_2d_feature_extraction 2D feature extraction To update https://github.com/bmcv Imaging 2d_feature_extraction imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ 0.1.1 pandas False +2d_filter_segmentation_by_features ip_2d_filter_segmentation_by_features filter segmentation by rules To update https://github.com/bmcv Imaging 2d_filter_segmentation_by_features imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ 0.0.1 scikit-image False +2d_histogram_equalization ip_histogram_equalization 2d histogram equalization To update https://github.com/bmcv Imaging 2d_histogram_equalization imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ 0.0.1 scikit-image False +2d_simple_filter ip_filter_standard 2d simple filter To update https://github.com/bmcv Imaging 2d_simple_filter imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ 0.0.3 scikit-image False +2d_split_binaryimage_by_watershed ip_2d_split_binaryimage_by_watershed split object by watershed To update https://github.com/bmcv Imaging 2d_split_binaryimage_by_watershed imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_split_binaryimage_by_watershed/ 0.0.1 scikit-image False +3d_tensor_feature_dimension_reduction ip_3d_tensor_feature_dimension_reduction Dimensionality reduction for features (channels) of 3D tensor data using UMAP To update https://github.com/BMCV/galaxy-image-analysis Imaging 3d_tensor_feature_dimension_reduction imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/ 0.0.1 numpy False +anisotropic_diffusion ip_anisotropic_diffusion Anisotropic image diffusion To update https://github.com/bmcv Imaging anisotropic_diffusion imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ 0.2 scikit-image False +bfconvert ip_convertimage Convert image To update https://github.com/bmcv Imaging, Convert Formats bfconvert imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ 6.7.0+galaxy1 bftools 6.7.0 False +binary2labelimage ip_binary_to_labelimage Binary 2 label image To update https://github.com/bmcv Imaging binary2labelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ 0.4 scikit-image False +binaryimage2points ip_binaryimage_to_points Binary Image to Points To update https://github.com/bmcv Imaging binaryimage2points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ 0.1 numpy False +color-deconvolution ip_color_deconvolution Color-deconvolution methods To update https://github.com/bmcv Imaging color_deconvolution imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/ 0.8 scikit-image False +concat_channels ip_concat_channels Concatenate images To update https://github.com/bmcv Imaging concat_channels imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ 0.2 scikit-image False +coordinates_of_roi ip_coordinates_of_roi Coordinates of ROI To update https://github.com/bmcv Imaging coordinates_of_roi imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ 0.0.4 scikit-image False +count_objects ip_count_objects Count Objects To update https://github.com/bmcv Imaging count_objects imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ 0.0.5 scikit-image False +curve_fitting ip_curve_fitting Polynomial curve fitting to data points To update https://github.com/BMCV/galaxy-image-analysis Imaging curve_fitting imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ 0.0.3 numpy False +detection_viz ip_detection_viz Detection Visualization To update https://github.com/bmcv Imaging detection_viz imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ 0.3 scikit-image False +image_info ip_imageinfo Extracts image metadata To update https://github.com/bmcv Imaging image_info imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ 0.2 bftools 6.7.0 False +image_registration_affine ip_image_registration Intensity-based Image Registration To update https://github.com/bmcv Imaging image_registration_affine imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ 0.0.3 scikit-image False +imagecoordinates_flipaxis imagecoordinates_flipaxis Flip coordinate axes To update https://github.com/bmcv Imaging imagecoordinates_flipaxis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ 0.1 pandas False +labelimage2points ip_labelimage_to_points Label Image to Points To update https://github.com/bmcv Imaging labelimage2points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ 0.2 scikit-image False +landmark_registration ip_landmark_registration Landmark Registration To update https://github.com/bmcv Imaging landmark_registration imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ 0.1.0 scikit-image False +mahotas-features ip_mahotas_features Compute image features using mahotas. To update https://github.com/luispedro/mahotas Imaging mahotas_features imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ 0.7 mahotas False +mergeneighboursinlabelimage ip_merge_neighbours_in_label Merge Neighbours in Label Image To update https://github.com/bmcv Imaging mergeneighboursinlabelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage 0.3 scikit-image False +overlay_images ip_overlay_images Overlay two images To update https://github.com/BMCV/galaxy-image-analysis Imaging overlay_images imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ 0.0.3 scikit-image False +permutate_axis ip_permutate_axis Permutates axes To update https://github.com/bmcv Imaging permutate_axis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ 0.2 scikit-image False +points2binaryimage ip_points_to_binaryimage Points to Binary Image To update https://github.com/bmcv Imaging points2binaryimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ 0.2 scikit-image False +points2labelimage ip_points_to_label Points to label image To update https://github.com/bmcv Imaging points2labelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ 0.3 numpy False +points_association_nn ip_points_association_nn Association of points in consecutive frames To update https://github.com/BMCV/galaxy-image-analysis Imaging points_association_nn imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ 0.0.3 numpy False +projective_transformation ip_projective_transformation Projective transformation To update https://github.com/bmcv Imaging projective_transformation imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ 0.1.2 scikit-image False +projective_transformation_points ip_projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates To update https://github.com/bmcv Imaging projective_transformation_points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ 0.1.1 scikit-image False +scale_image ip_scale_image Scale image To update https://github.com/bmcv Imaging scale_image imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ 0.4 pillow False +segmetrics ip_segmetrics Image segmentation and object detection performance measures To update https://github.com/bmcv Imaging segmetrics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ 1.4.0-1 segmetrics 1.4 False +slice_image ip_slice_image Slice image To update https://github.com/bmcv Imaging slice_image imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ 0.3 scikit-image False +split_labelmap ip_split_labelmap Split Labelmaps To update https://github.com/bmcv Imaging split_labelmap imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ 0.2 scikit-image False +spot_detection_2d ip_spot_detection_2d Spot detection in 2D image sequence To update https://github.com/BMCV/galaxy-image-analysis Imaging spot_detection_2d imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ 0.0.3 imageio False +superdsm ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images Up-to-date https://github.com/bmcv Imaging superdsm imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ 0.1.3 superdsm 0.1.3 False +visceral-evaluatesegmentation ip_visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool To update https://github.com/bmcv Imaging visceral_evaluatesegmentation imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation 0.5 visceral-evaluatesegmentation 2015.07.03 False +wsi_extract_top_view ip_wsi_extract_top_view WSI Extract Top View To update https://github.com/bmcv Imaging wsi_extract_top_view imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ 0.2 scikit-image False +cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper To update Imaging cellprofiler bgruening https://github.com/bgruening/galaxytools/tree/master/tools False +cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update Imaging cellprofiler4 bgruening https://github.com/bgruening/galaxytools/tree/master/tools 4.2.1 False +graphicsmagick graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ 1.3.31 graphicsmagick 1.3.26 False +imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. To update http://fiji.sc Imaging imagej2 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 False +spyboat spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat 0.1.2 spyboat False +qupath_roi_splitter qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter galaxyp hhttps://github.com/npinter/ROIsplitter 0.1.0+galaxy1 geojson False +hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack To update Imaging hyperstack_to_bleach_corrected_movie lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 20230328 Fiji 20220414 False +incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server To update Imaging incucyte_stack_and_upload_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero 20230824 Fiji 20220414 False +measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update Imaging measure_gastruloids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 20221216 fiji 20220414 False +omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update Imaging omero_clean_rois_tables lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 20230623 fiji 20220414 False +omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 fiji 20220414 False +omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 20230728 fiji 20220414 False +upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0.0.5 omero-py 5.11.1 False diff --git a/results/index.html b/results/index.html new file mode 100644 index 00000000..6e21d862 --- /dev/null +++ b/results/index.html @@ -0,0 +1,25963 @@ + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ExpandGalaxy wrapper idGalaxy wrapper versionConda versionConda idStatusbio.tool idbio.tool nameEDAM operationEDAM topicDescriptionbio.tool descriptionStatusSourceToolShed categoriesToolShed idGalaxy wrapper ownerGalaxy wrapper source
askor0.23.56.2bioconductor-limmaTo updateAskoR links EdgeR and AskOmicsTo updatehttps://github.com/askomics/askoRTranscriptomicsaskor_degenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/askor
baric_archive1.1.0To updateA data source tool to fetch data from a BARIC Archive server.To updatehttps://www.cesgo.org/catibaric/Data Sourcegenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive
braker2.1.6To updateBRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .To updatehttps://github.com/Gaius-Augustus/BRAKERGenome annotationbrakergenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/braker
braker33.0.3To updateBRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .To updatehttps://github.com/Gaius-Augustus/BRAKERGenome annotationbraker3genouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/braker
feelnc2asko0.11.7.8perl-bioperlTo updateConvert FeelNC GTF to GFF3To updatehttps://github.com/tderrien/FEELncConvert Formatsfeelnc2askogenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko
gcms2isocor0.1.0openjdkTo updateConversion from GCMS PostRun Analysis to IsocorTo updateMetabolomicsgcms2isocorgenouest
get_pairs0.3pythonTo updateSeparate paired and unpaired reads from two fastq filesTo updateFastq Manipulationget_pairsgenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs
helixer0.3.2To updateGene calling with Deep Neural NetworksTo updatehttps://github.com/weberlab-hhu/HelixerGenome annotationhelixergenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/helixer
logol1.7.81.7.8logolUp-to-dateLogol is a pattern matching grammar language and a set of tools to search a pattern in a sequenceUp-to-datehttp://logol.genouest.org/web/app.php/logolSequence Analysisgenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/logol
meneco1.5.21.5.2menecoUp-to-dateMeneco computes minimal completions to your draft network with reactions from a repair networkUp-to-datehttp://bioasp.github.io/meneco/Systems Biologymenecogenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/meneco
miranda2asko0.2perlTo updateConverts miRanda output into AskOmics formatTo updateConvert Formatsmiranda2askogenouesthttps://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko
openlabcds2csv0.1.0openjdkTo updateCreates a summary of several "Internal Standard Report" OpenLabCDS results.To updateMetabolomicsopenlabcds2csvgenouest
peptimapper2.0To updateProteogenomics workflow for the expert annotation of eukaryotic genomesTo updatehttps://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9Proteomicsgenouest
Ensembl-REST0.1.2requestsTo updateA suite of Galaxy tools designed to work with Ensembl REST API.To updatehttps://rest.ensembl.orgData Sourceearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST
GAFA0.3.1To updateGene Align and Family AggregatorTo updatehttp://aequatus.tgac.ac.ukVisualizationgafaearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/
TreeBest1.9.2.post01.9.2.post0treebestUp-to-dateTreeBeST bestUp-to-datehttp://treesoft.sourceforge.net/treebest.shtmlPhylogeneticstreebest_bestearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest
apoc1.0+galaxy11b16apocTo updateLarge-scale structural comparison of protein pocketsTo updatehttp://cssb.biology.gatech.edu/APocComputational chemistryapocearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/
blast_parser0.1.2To updateConvert 12- or 24-column BLAST output into 3-column hcluster_sg inputTo updatehttps://github.com/TGAC/earlham-galaxytools/Phylogeneticsblast_parserearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser
ete3.1.23.1.1ete3To updateAnalyse phylogenetic trees using the ETE ToolkitTo updatehttp://etetoolkit.org/Phylogeneticseteearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete
export_to_cluster0.0.2EXPORT_DIR_PREFIXTo updateExport datasets to clusterTo updatehttps://github.com/TGAC/earlham-galaxytools/Data Exportexport_to_clusterearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/
gblocks0.91b0.91bgblocksUp-to-dateGblocksUp-to-datehttp://molevol.cmima.csic.es/castresana/Gblocks.htmlSequence Analysisgblocksearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks
gstf_preparation0.4.3pythonTo updateGeneSeqToFamily preparation converts data for the workflowTo updatehttps://github.com/TGAC/earlham-galaxytools/Convert Formatsgstf_preparationearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation
hcluster_sg0.5.1.10.5.1hcluster_sgTo updateHierarchically clustering on a sparse graphTo updatehttps://github.com/douglasgscofield/hclusterPhylogeneticshcluster_sgearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg
hcluster_sg_parser0.2.1To updateConverts hcluster_sg 3-column output into lists of idsTo updatehttps://github.com/TGAC/earlham-galaxytools/Phylogeneticshcluster_sg_parserearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser
lotus22.232.28lotus2To updatelotus2lotus2Sequence feature detectionMetagenomicsLotuS2 OTU processing pipelineLotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.To updatehttp://lotus2.earlham.ac.uk/Metagenomicslotus2earlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2
miranda3.3a+galaxy13.3amirandaTo updateFinds potential target sites for miRNAs in genomic sequencesTo updatehttp://www.microrna.org/RNAmirandaearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda
plotheatmap1.01.62.1bioconductor-preprocesscoreTo updateThis tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output.To updateComputational chemistryplotheatmapearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap
rdock1.02013.1rDockTo updateDocking ligands to proteins and nucleic acidsTo updatehttp://rdock.sourceforge.net/Computational chemistryrdockearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/
replace_chromosome_names0.1pythonTo updateReplace chromosome namesTo updateText Manipulationreplace_chromosome_namesearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/
rsat_filter_snps0.1To updateFilter SNPs in RSAT Matrix Scan outputTo updatehttps://github.com/TGAC/earlham-galaxytools/ChIP-seq, Systems Biologyrsat_filter_snpsearlhamhttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps
smart_domains0.1.01.7.8perl-bioperlTo updateSMART domainsTo updatehttp://smart.embl.de/Sequence Analysissmart_domainsearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains
smina1.02017.11.9sminaTo updatesmina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimizationTo updatehttps://sourceforge.net/projects/smina/Computational chemistrysminaearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/
t_coffee13.45.0.484626413.46.0.919e8c6bt-coffeeTo updateT-CoffeeTo updatehttp://www.tcoffee.org/Sequence Analysist_coffeeearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee
abacas1.13.23mummerTo updateOrder and Orientate ContigsTo updatehttps://github.com/phac-nml/abacasAssemblyabacasnmlhttps://github.com/phac-nml/abacas
assemblystats1.1.01.7.8perl-bioperlTo updateSummarise an assembly (e.g. N50 metrics)To updatehttps://github.com/phac-nml/galaxy_toolsAssemblyassemblystatsnmlhttps://github.com/phac-nml/galaxy_tools
bam2mappingstats1.1.0perlTo updateGenerates mapping stats from a bam file.To updatehttps://github.com/phac-nml/galaxy_toolsAssemblybam2mappingstatsnmlhttps://github.com/phac-nml/galaxy_tools
bamclipper1.0.01.0.0bamclipperUp-to-dateSoft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.Up-to-datehttps://github.com/tommyau/bamclipperSequence Analysisbamclippernmlhttps://github.com/tommyau/bamclipper
biohansel2.4.02.6.1bio_hanselTo updateHeidelberg and Enteritidis SNP ElucidationTo updatehttps://github.com/phac-nml/biohanselSequence Analysisbiohanselnmlhttps://github.com/phac-nml/biohansel
biohansel_bionumeric_converter0.2.0pandasTo updateConvert BioHansel output data to a Bionumerics friendly formTo updatehttps://github.com/phac-nml/galaxy_toolsText Manipulationbiohansel_bionumeric_converternml
bundle_collections1.3.02.54perl-getopt-longTo updateTool to bundle up list collection into a single zip to be downloadTo updateSequence Analysisbundle_collectionsnml
collapse_collection5.1.0gawkTo updateCollection tool that collapses a list of files into a single datasset in order of appears in collectionTo updateSequence Analysiscollapse_collectionsnml
combineJSON0.1To updateJSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.To updateSequence Analysiscombine_jsonnml
combine_assembly_stats1.02.54perl-getopt-longTo updateCombine multiple Assemblystats datasets into a single tabular reportTo updatehttps://github.com/phac-nml/galaxy_toolsAssemblycombine_assemblystatsnmlhttps://github.com/phac-nml/galaxy_tools
combine_tabular_collection0.1To updateCombine Tabular Collection into a single fileTo updateSequence Analysiscombine_tabular_collectionnml
concat_paired0.2To updateConcatenate paired datasetsTo updatehttps://github.com/phac-nml/concatText Manipulationconcat_pairednmlhttps://github.com/phac-nml/concat
cryptogenotyper1.01.0cryptogenotyperUp-to-dateCryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers.Up-to-datehttps://github.com/phac-nml/CryptoGenotyperSequence Analysiscryptogenotypernmlhttps://github.com/phac-nml/CryptoGenotyper
csvtk0.20.00.28.0csvtkTo updateRapid data investigation and manipulation of csv/tsv filesTo updatehttps://bioinf.shenwei.me/csvtk/Text Manipulationcsvtknmlhttps://github.com/shenwei356/csvtk
ectyper1.0.01.0.0ectyperUp-to-dateEC-Typer - in silico serotyping of Escherichia coli speciesUp-to-datehttps://github.com/phac-nml/ecoli_serotypingSequence Analysisectypernmlhttps://github.com/phac-nml/ecoli_serotyping
fasta2bed1.0.01.7.8perl-bioperlTo updateConvert multiple fasta file into tabular bed file formatTo updatehttps://github.com/phac-nml/galaxy_toolsSequence Analysisfasta2bednmlhttps://github.com/phac-nml/galaxy_tools
fasta_extract1.1.01.7.8perl-bioperlTo updateextract single fasta from multiple fasta fileTo updatehttps://toolshed.g2.bx.psu.edu/view/nml/fasta_extractSequence Analysisfasta_extractnmlhttps://toolshed.g2.bx.psu.edu/view/nml/fasta_extract
fastqc_stats1.21.7.8perl-bioperlTo updateSummary multiple FastQC into a single tabular line reportTo updatehttps://github.com/phac-nml/galaxy_toolsSequence Analysisfastqc_statsnmlhttps://github.com/phac-nml/galaxy_tools
feht0.1.01.1.0fehtTo updateAutomatically identify makers predictive of groups.To updatehttps://github.com/phac-nml/galaxy_toolsSequence Analysisfehtnmlhttps://github.com/phac-nml/galaxy_tools
filter_spades_repeats1.0.11.7.8perl-bioperlTo updateRemove short and repeat contigs/scaffoldsTo updatehttps://github.com/phac-nml/galaxy_tools/Assemblyfilter_spades_repeatsnmlhttps://github.com/phac-nml/galaxy_tools/
getmlst0.1.4.10.2.0srst2To updateDownload MLST datasets by species from pubmlst.orgTo updateSequence Analysisgetmlstnml
gnali1.1.01.1.0gnaliUp-to-dateA tool to find nonessential, loss-of-function gene variantsUp-to-datehttps://github.com/phac-nml/gnali/Variant Analysisgnalinmlhttps://github.com/phac-nml/gnali/
hivtrace1.0.11.5.0hivtraceTo updateAn application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.To updateSequence Analysishivtracenmlhttps://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace
kaptive0.3.02.0.6kaptiveTo updateKaptive reports information about capsular (K) loci found in genome assemblies.To updateSequence Analysiskaptivenml
kat_filter2.32.4.2katTo updateFiltering kmers or reads from a database of kmers hashesTo updateSequence Analysiskat_filternml
kat_sect2.32.4.2katTo updateSEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.To updatekat_sectnml
mauve_contig_mover1.0.102.4.0.r4736mauveTo updateOrder a draft genome relative to a related reference genomeTo updatehttps://github.com/phac-nml/mauve_contig_moverSequence Analysismauve_contig_movernmlhttps://github.com/phac-nml/mauve_contig_mover
mob_suite3.0.33.1.7mob_suiteTo updateMOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assembliesTo updatehttps://github.com/phac-nml/mob-suiteSequence Analysismob_suitenmlhttps://github.com/phac-nml/mob-suite
mrbayes1.0.23.2.7mrbayesTo updateA program for the Bayesian estimation of phylogeny.To updateSequence Analysismrbayesnml
mykrobe_parser0.1.4.1r-baseTo updateRScript to parse the results of mykrobe predictor.To updatehttps://github.com/phac-nml/mykrobe-parserSequence Analysismykrobe_parsernmlhttps://github.com/phac-nml/mykrobe-parser
pangolin1.1.144.3pangolinTo updatePhylogenetic Assignment of Named Global Outbreak LINeagesTo updatehttps://github.com/hCoV-2019/pangolinSequence Analysispangolinnmlhttps://github.com/hCoV-2019/pangolin
patrist0.1.2pythonTo updateExtract Patristic Distance From a TreeTo updatehttps://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02Phylogeneticspatristnmlhttps://github.com/phac-nml/patrist
plasmid_profiler0.1.6rTo updateExplores plasmid content in WGS dataTo updateplasmid_profilernml
plasmid_profiler_suiteTo updatePlasmid Profiler suite defining all dependencies for Plasmid ProfilerTo updateSequence Analysissuite_plasmid_profilernml
plasmidspades1.13.15.5spadesTo updateGenome assembler for assemblying plasmidTo updateAssemblyplasmidspadesnml
pneumocat1.2.11.2.1pneumocatUp-to-datePneumococcal Capsular Typing of illumina fastq readsUp-to-datehttps://github.com/phe-bioinformatics/PneumoCaTVariant Analysispneumocatnmlhttps://github.com/phe-bioinformatics/PneumoCaT
promer1.2pythonTo updateAligns two sets of contigs and reports amino acid substitutions between themTo updatehttps://github.com/phac-nml/promerAssemblypromernmlhttps://github.com/phac-nml/promer
pseudogenome1.0.01.7.8perl-bioperlTo updateCreate a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.To updatehttps://github.com/phac-nml/galaxy_toolsSequence Analysispseudogenomenml
quasitools0.7.00.7.0quasitoolsUp-to-dateA collection of tools for analysing Viral QuasispeciesUp-to-datehttps://github.com/phac-nml/quasitoolsSequence Analysisquasitoolsnmlhttps://github.com/phac-nml/quasitools
refseq_masher0.1.20.1.2refseq_masherUp-to-dateFind what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.Up-to-datehttps://github.com/phac-nml/refseq_masherSequence Analysisrefseq_mashernmlhttps://github.com/phac-nml/refseq_masher
seqtk_nml1.0.11.4seqtkTo updateTool to downsample fastq readsTo updatehttps://github.com/lh3/seqtkSequence Analysisseqtk_nmlnmlhttps://github.com/phac-nml/snvphyl-galaxy
sistr_cmd1.1.11.1.1sistr_cmdUp-to-dateSISTR in silico serotyping toolUp-to-datehttps://github.com/phac-nml/sistr_cmdSequence Analysissistr_cmdnml
smalt0.7.60.7.6smaltUp-to-dateSMALT aligns DNA sequencing reads with a reference genome.Up-to-datehttp://www.sanger.ac.uk/science/tools/smalt-0Sequence Analysissmaltnmlhttps://sourceforge.net/projects/smalt/
spades_header_fixer1.1.2+galaxy1sedTo updateFixes Spades Fasta idsTo updatehttps://github.com/phac-nml/galaxy_toolsFasta Manipulationspades_fasta_header_fixernmlhttps://github.com/phac-nml/galaxy_tools
spatyper0.3.30.3.3spatyperUp-to-dateDetermines SPA type based on repeats in a submitted staphylococcal protein A fasta file.Up-to-datehttps://github.com/HCGB-IGTP/spaTyperSequence Analysisspatypernmlhttps://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper
spolpred1.0.1spolpredTo updateA program for predicting the spoligotype from raw sequence readsTo updateSequence Analysisspolprednml
srst20.3.70.2.0srst2To updateShort Read Sequence Typing for Bacterial PathogensTo updateSequence Analysissrst2nml
staramr0.10.00.10.0staramrUp-to-dateScan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.Up-to-datehttps://github.com/phac-nml/staramrSequence Analysisstaramrnmlhttps://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr
stringmlst1.1.00.6.3stringMLSTTo updateRapid and accurate identification of the sequence type (ST)To updateSequence Analysisstringmlstnml
tree_relabeler1.1.01.7.8perl-bioperlTo updateRelabels the tips of a newick formatted tree.To updateText Manipulationtree_relabelernmlhttps://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler
wade0.2.5+galaxy10.2.6wadeTo updateidentify regions of interestTo updatehttps://github.com/phac-nml/wadeSequence Analysiswadenmlhttps://github.com/phac-nml/wade
camera1.48.00.4_1r-snowTo updateTo updateMetabolomicscameraworkflow4metabolomics
correlation_analysis1.0.1+galaxy01.1_4r-batchTo update[Metabolomics][W4M] Metabolites Correlation AnalysisTo updatehttp://workflow4metabolomics.orgMetabolomicscorrelation_analysisworkflow4metabolomicshttps://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/
genformr8genformTo updategenform: generation of molecular formulas by high-resolution MS and MS/MS dataTo updatehttps://sourceforge.net/projects/genform/Metabolomicsgenformworkflow4metabolomicshttps://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/
influx_si5.1.07.0.1influx_siTo updatemetabolic flux estimation based on [in]stationary labelingTo updatehttps://github.com/sgsokol/influxMetabolomicsinflux_siworkflow4metabolomicshttps://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/
ipo1.10.01.26.0bioconductor-ipoTo update[W4M][LC-MS] IPOTo updatehttps://github.com/rietho/IPOMetabolomicsipolecorguillehttps://github.com/rietho/IPO
isoplot1.3.0+galaxy11.3.1isoplotTo updateIsoplot is a software for the visualisation of MS data from C13 labelling experimentsTo updateMetabolomics, Visualizationisoplotworkflow4metabolomicshttps://github.com/llegregam/Isoplot/tree/main
kmd_hmdb_data_plot1.0.0pythonTo updateretrieves data from KMD HMDB API and produce plot and csv fileTo updatehttps://github.com/workflow4metabolomics/tools-metabolomicsMetabolomicskmd_hmdb_data_plotworkflow4metabolomicshttps://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/
mixmodel4repeated_measures3.1.0r-lme4To update[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed modelTo updatehttp://workflow4metabolomics.orgMetabolomicsmixmodel4repeated_measuresworkflow4metabolomicshttps://github.com/workflow4metabolomics/tools-metabolomics
ms2snoop2.2.1r-baseTo update[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity.To updatehttp://workflow4metabolomics.orgMetabolomicsms2snoopworkflow4metabolomics
nmr_annotation3.0.01.1_4r-batchTo update[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimationTo updatehttp://workflow4metabolomics.orgMetabolomicsnmr_annotationmarie-tremblay-metatoulhttps://github.com/workflow4metabolomics/nmr_annotation
nmr_annotation2d2.0.01.1_4r-batchTo update[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectraTo updatehttp://workflow4metabolomics.orgMetabolomics2dnmrannotationmarie-tremblay-metatoulhttps://github.com/workflow4metabolomics/tools-metabolomics
nmr_preprocessing1.1_4r-batchTo update[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correctionTo updatehttp://workflow4metabolomics.orgMetabolomicsnmr_preprocessingmarie-tremblay-metatoulhttps://github.com/workflow4metabolomics/nmr_preprocessing
normalization1.0.71.1_4r-batchTo update[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed dataTo updatehttp://workflow4metabolomics.orgMetabolomicsnormalizationmarie-tremblay-metatoulhttps://github.com/workflow4metabolomics/normalization
physiofit2.2.12.2.1physiofit4galaxyUp-to-datePhysioFit is a scientific tool designed to i) quantify exchange (production and consumption) fluxes and ii) cell growth rate during (batch) cultivations of microorganisms. Fluxes are estimated from time-course measurements of extracellular metabolites and biomass concentrations. PhysioFit has been designed to calculate fluxes in batch experiments, assuming cells are in metabolic (pseudo) steady-state (i.e. fluxes are constant during the experiment).Up-to-dateMetabolomicsphysiofitworkflow4metabolomicshttps://github.com/MetaSys-LISBP/PhysioFit
physiofit_manager1.0.11.0.1physiofit_data_managerUp-to-dateHandling of physiofit input filesUp-to-datehttps://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_ManagerMetabolomicsphysiofit_managerworkflow4metabolomics
xcms3.12.03.22.0bioconductor-xcmsTo updateTo updatehttps://github.com/sneumann/xcmsMetabolomicsxcmsworkflow4metabolomicshttps://github.com/workflow4metabolomics/tools-metabolomics/
apollo4.2.13apolloTo updateAccess an Apollo instance from GalaxyTo updatehttps://github.com/galaxy-genome-annotation/python-apolloWeb Servicesggahttps://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo
askomics0.5askocliTo updateGalaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/To updatehttps://github.com/askomics/Web Servicesggahttps://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics
chado2.3.9python-chadoTo updateGalaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chadoTo updatehttps://github.com/galaxy-genome-annotation/python-chadoWeb Servicesggahttps://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado
genenotebook0.4.80.4.8genobooUp-to-dateGalaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.ioUp-to-datehttps://genenotebook.github.ioWeb Servicesggahttps://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook
jbrowsepythonTo updateA tool allowing to export a JBrowse dataset into a JBrowse docker containerTo updatehttps://jbrowse.orgWeb Servicesjbrowse_to_containerggahttps://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse
tripal3.2.1python-tripalTo updateGalaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripalTo updatehttps://github.com/galaxy-genome-annotation/python-tripalWeb Servicesggahttps://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal
w4mcorcov0.98.18r-baseTo updateOPLS-DA Contrasts of Univariate ResultsTo updatehttps://github.com/HegemanLab/w4mcorcov_galaxy_wrapperMetabolomicsw4mcorcoveschen42https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master
w4mclassfilter0.98.19r-baseTo updateFilter W4M data by values or metadataTo updatehttps://github.com/HegemanLab/w4mclassfilter_galaxy_wrapperMetabolomicsw4mclassfiltereschen42https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master
w4mjoinpn0.98.28.25coreutilsTo updateJoin positive- and negative-mode W4M datasetsTo updatehttps://github.com/HegemanLab/w4mjoinpn_galaxy_wrapperMetabolomicsw4mjoinpneschen42https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master
2d_auto_threshold0.0.5scikit-imageTo updateAutomatic thresholdingTo updatehttps://github.com/bmcvImaging2d_auto_thresholdimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/
2d_feature_extraction0.1.1pandasTo update2D feature extractionTo updatehttps://github.com/bmcvImaging2d_feature_extractionimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/
2d_filter_segmentation_by_features0.0.1scikit-imageTo updatefilter segmentation by rulesTo updatehttps://github.com/bmcvImaging2d_filter_segmentation_by_featuresimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/
2d_histogram_equalization0.0.1scikit-imageTo update2d histogram equalizationTo updatehttps://github.com/bmcvImaging2d_histogram_equalizationimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/
2d_simple_filter0.0.3scikit-imageTo update2d simple filterTo updatehttps://github.com/bmcvImaging2d_simple_filterimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/
2d_split_binaryimage_by_watershed0.0.1scikit-imageTo updatesplit object by watershedTo updatehttps://github.com/bmcvImaging2d_split_binaryimage_by_watershedimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_split_binaryimage_by_watershed/
3d_tensor_feature_dimension_reduction0.0.1numpyTo updateDimensionality reduction for features (channels) of 3D tensor data using UMAPTo updatehttps://github.com/BMCV/galaxy-image-analysisImaging3d_tensor_feature_dimension_reductionimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/
anisotropic_diffusion0.2scikit-imageTo updateAnisotropic image diffusionTo updatehttps://github.com/bmcvImaginganisotropic_diffusionimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/
bfconvert6.7.0+galaxy16.7.0bftoolsTo updateConvert imageTo updatehttps://github.com/bmcvImaging, Convert Formatsbfconvertimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/
binary2labelimage0.4scikit-imageTo updateBinary 2 label imageTo updatehttps://github.com/bmcvImagingbinary2labelimageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/
binaryimage2points0.1numpyTo updateBinary Image to PointsTo updatehttps://github.com/bmcvImagingbinaryimage2pointsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/
color-deconvolution0.8scikit-imageTo updateColor-deconvolution methodsTo updatehttps://github.com/bmcvImagingcolor_deconvolutionimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/
concat_channels0.2scikit-imageTo updateConcatenate imagesTo updatehttps://github.com/bmcvImagingconcat_channelsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/
coordinates_of_roi0.0.4scikit-imageTo updateCoordinates of ROITo updatehttps://github.com/bmcvImagingcoordinates_of_roiimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/
count_objects0.0.5scikit-imageTo updateCount ObjectsTo updatehttps://github.com/bmcvImagingcount_objectsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/
curl_post0.0.2curlTo updateSend file via cURL POSTTo updatehttps://github.com/bmcvData Export, Web Servicescurl_postimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post
curve_fitting0.0.3numpyTo updatePolynomial curve fitting to data pointsTo updatehttps://github.com/BMCV/galaxy-image-analysisImagingcurve_fittingimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/
detection_viz0.3scikit-imageTo updateDetection VisualizationTo updatehttps://github.com/bmcvImagingdetection_vizimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/
image_info0.26.7.0bftoolsTo updateExtracts image metadataTo updatehttps://github.com/bmcvImagingimage_infoimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/
image_registration_affine0.0.3scikit-imageTo updateIntensity-based Image RegistrationTo updatehttps://github.com/bmcvImagingimage_registration_affineimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/
imagecoordinates_flipaxis0.1pandasTo updateFlip coordinate axesTo updatehttps://github.com/bmcvImagingimagecoordinates_flipaxisimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/
labelimage2points0.2scikit-imageTo updateLabel Image to PointsTo updatehttps://github.com/bmcvImaginglabelimage2pointsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/
landmark_registration0.1.0scikit-imageTo updateLandmark RegistrationTo updatehttps://github.com/bmcvImaginglandmark_registrationimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/
mahotas-features0.7mahotasTo updateCompute image features using mahotas.To updatehttps://github.com/luispedro/mahotasImagingmahotas_featuresimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/
mergeneighboursinlabelimage0.3scikit-imageTo updateMerge Neighbours in Label ImageTo updatehttps://github.com/bmcvImagingmergeneighboursinlabelimageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage
overlay_images0.0.3scikit-imageTo updateOverlay two imagesTo updatehttps://github.com/BMCV/galaxy-image-analysisImagingoverlay_imagesimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/
permutate_axis0.2scikit-imageTo updatePermutates axesTo updatehttps://github.com/bmcvImagingpermutate_axisimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/
points2binaryimage0.2scikit-imageTo updatePoints to Binary ImageTo updatehttps://github.com/bmcvImagingpoints2binaryimageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/
points2labelimage0.3numpyTo updatePoints to label imageTo updatehttps://github.com/bmcvImagingpoints2labelimageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/
points_association_nn0.0.3numpyTo updateAssociation of points in consecutive framesTo updatehttps://github.com/BMCV/galaxy-image-analysisImagingpoints_association_nnimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/
projective_transformation0.1.2scikit-imageTo updateProjective transformationTo updatehttps://github.com/bmcvImagingprojective_transformationimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/
projective_transformation_points0.1.1scikit-imageTo updateProjective transformation of ROIs defined by pixel (point) coordinatesTo updatehttps://github.com/bmcvImagingprojective_transformation_pointsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/
scale_image0.4pillowTo updateScale imageTo updatehttps://github.com/bmcvImagingscale_imageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/
segmetrics1.4.0-11.4segmetricsTo updateImage segmentation and object detection performance measuresTo updatehttps://github.com/bmcvImagingsegmetricsimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/
slice_image0.3scikit-imageTo updateSlice imageTo updatehttps://github.com/bmcvImagingslice_imageimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/
split_labelmap0.2scikit-imageTo updateSplit LabelmapsTo updatehttps://github.com/bmcvImagingsplit_labelmapimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/
spot_detection_2d0.0.3imageioTo updateSpot detection in 2D image sequenceTo updatehttps://github.com/BMCV/galaxy-image-analysisImagingspot_detection_2dimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/
superdsm0.1.30.1.3superdsmUp-to-dateGlobally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy imagesUp-to-datehttps://github.com/bmcvImagingsuperdsmimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/
unzip6.0unzipTo updateUnzip fileTo updatehttps://github.com/bmcvConvert Formatsunzipimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/
visceral-evaluatesegmentation0.52015.07.03visceral-evaluatesegmentationTo updateVisceral Project - Evaluate Segmentation ToolTo updatehttps://github.com/bmcvImagingvisceral_evaluatesegmentationimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation
wsi_extract_top_view0.2scikit-imageTo updateWSI Extract Top ViewTo updatehttps://github.com/bmcvImagingwsi_extract_top_viewimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/
add_value1.0.1perlTo updateAdd a value as a new column.To updateText Manipulationadd_valuedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value
annotation_profiler1.0.00.10.0bx-pythonTo updateProfile Annotations for a set of genomic intervalsTo updateGenomic Interval Operationsannotation_profilerdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/annotation_profiler
best_regression_subsets1.0.0numpyTo updatePerform Best-subsets RegressionTo updateSequence Analysis, Variant Analysisbest_regression_subsetsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets
blat_coverage_report1.0.0To updatePolymorphism of the ReadsTo updateNext Gen Mappers, Sequence Analysisblat_coverage_reportdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report
blat_mapping1.0.0To updateCoverage of the Reads in wiggle formatTo updateNext Gen Mappers, Sequence Analysisblat_mappingdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping
bowtie_wrappers1.2.01.3.1bowtieTo updateGalaxy wrappers for the Bowtie short read mapping tools.To updatehttp://bowtie-bio.sourceforge.net/Next Gen Mappersbowtie_wrappersdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers
canonical_correlation_analysis1.0.0RTo updateCanonical Correlation AnalysisTo updateStatisticscanonical_correlation_analysisdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis
categorize_elements_satisfying_criteria1.0.0To updateCategorize Elements satisfying criteria.To updateStatisticscategorize_elements_satisfying_criteriadevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria
ccat0.0.23.0ccatTo updateControl-based ChIP-seq Analysis ToolTo updateChIP-seqccatdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat
cd_hit_dup0.0.14.8.1cd-hit-auxtoolsTo updatesimple tool for removing duplicates from sequencing readsTo updateMetagenomics, Sequence Analysiscd_hit_dupdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup
change_case1.0.1perlTo updateConvert column case.To updateText Manipulationchange_casedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case
compute_motif_frequencies_for_all_motifs1.0.0To updateCompute Motif Frequencies For All Motifs, motif by motif.To updateSequence Analysis, Statisticscompute_motif_frequencies_for_all_motifsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs
compute_motifs_frequency1.0.0To updateCompute Motif Frequencies in indel flanking regions.To updateSequence Analysis, Statisticscompute_motifs_frequencydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency
compute_q_values1.0.1RTo updateCompute q-values based on multiple simultaneous tests p-valuesTo updateStatisticscompute_q_valuesdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values
condense_characters1.0.0To updateCondense consecutive characters.To updateText Manipulationcondense_charactersdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters
convert_characters1.0.1pythonTo updateConvert delimiters to tab.To updateText Manipulationconvert_charactersdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters
convert_solid_color2nuc1.0.0To updateConvert Color Space to NucleotidesTo updateFasta Manipulationconvert_solid_color2nucdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc
correlation1.0.0rpyTo updateCorrelation for numeric columnsTo updateStatisticscorrelationdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation
count_gff_features0.21.1.0galaxy-opsTo updateCount GFF FeaturesTo updateSequence Analysiscount_gff_featuresdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features
ctd_batch1.0.0To updateCTD analysis of chemicals, diseases, or genesTo updateSequence Analysisctd_batchdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch
cummerbund2.16.0fonts-conda-ecosystemTo updateWrapper for the Bioconductor cummeRbund libraryTo updatehttps://bioconductor.org/packages/release/bioc/html/cummeRbund.htmlRNA, Visualizationcummerbunddevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund
cummerbund_to_tabular1.0.1To updateRegenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.To updateConvert Formats, Next Gen Mapperscummerbund_to_tabulardevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular
cut_columns1.0.2To updateSelect columns from a dataset.To updateText Manipulationcut_columnsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns
delete_overlapping_indels1.0.0To updateDelete Overlapping Indels from a chromosome indels fileTo updateSequence Analysisdelete_overlapping_indelsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels
dgidb_annotator0.1To updateAnnotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)To updateSystems Biology, Variant Analysisdgidb_annotatordevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator
divide_pg_snp1.0.0To updateSeparate pgSnp alleles into columnsTo updateSequence Analysisdivide_pg_snpdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp
draw_stacked_barplots1.0.0RTo updateDraw Stacked Bar Plots for different categories and different criteriaTo updateGraphics, Statisticsdraw_stacked_barplotsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots
dwt_cor_ava_perclass1.0.11.7.5r-waveslimTo updateCompute P-values and Correlation Coefficients for Feature OccurrencesTo updateStatisticsdwt_cor_ava_perclassdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass
dwt_cor_avb_all1.0.11.7.5r-waveslimTo updateCompute P-values and Correlation Coefficients for Occurrences of Two Set of FeaturesTo updateStatisticsdwt_cor_avb_alldevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all
dwt_ivc_all1.0.11.7.5r-waveslimTo updateCompute P-values and Second Moments for Feature OccurrencesTo updateStatisticsdwt_ivc_alldevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all
dwt_var_perclass1.0.11.7.5r-waveslimTo updateCompute P-values and Max Variances for Feature OccurrencesTo updateStatisticsdwt_var_perclassdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass
dwt_var_perfeature1.0.2r-bitopsTo updateWavelet variance using Discrete Wavelet TransfomsTo updateStatisticsdwt_var_perfeaturedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature
express1.1.11.5.1eXpressTo updateQuantify the abundances of a set of target sequences from sampled subsequencesTo updateRNAexpressdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/express
fasta_compute_length1.0.3pythonTo updateCompute sequence lengthTo updateFasta Manipulationfasta_compute_lengthdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length
fasta_concatenate_by_species0.0.10.10.0bx-pythonTo updateConcatenate FASTA alignment by speciesTo updateFasta Manipulationfasta_concatenate_by_speciesdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species
fasta_filter_by_length1.2pythonTo updateFilter sequences by lengthTo updateFasta Manipulationfasta_filter_by_lengthdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length
fasta_to_tabular1.1.1pythonTo updateFASTA-to-Tabular converterTo updateFasta Manipulationfasta_to_tabulardevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular
fastq_trimmer_by_quality1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ Quality Trimmer by sliding windowUp-to-dateFastq Manipulationfastq_trimmer_by_qualitydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality
fastqsolexa_to_fasta_qual1.0.0To updateFASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA dataTo updateConvert Formats, Fastq Manipulationfastqsolexa_to_fasta_qualdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual
featurecounter2.0.00.10.0bx-pythonTo updateFeature coverageTo updateSequence Analysis, Variant Analysisfeaturecounterdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter
filter_transcripts_via_tracking0.1To updateFilter Combined TranscriptsTo updateRNAfilter_transcripts_via_trackingdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking
generate_pc_lda_matrix1.0.0To updateGenerate a Matrix for using PC and LDATo updateSequence Analysisgenerate_pc_lda_matrixdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix
getindelrates_3way1.0.00.10.0bx-pythonTo updateEstimate Indel Rates for 3-way alignmentsTo updateSequence Analysis, Variant Analysisgetindelrates_3waydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way
getindels_2way1.0.0numpyTo updateFetch Indels from pairwise alignmentsTo updateSequence Analysis, Variant Analysisgetindels_2waydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way
gmaj2.0.1To updateGMAJ Multiple Alignment ViewerTo updateVisualizationgmajdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj
hisat1.0.3hisatTo updateHISAT is a fast and sensitive spliced alignment program.To updatehttp://ccb.jhu.edu/software/hisat/index.shtmlAssemblyhisatdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat
histogram1.0.42.7.8rpy2To updateHistogram of a numeric columnTo updateGraphics, Statisticshistogramdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram
indels_3way1.0.3To updateFetch Indels from 3-way alignmentsTo updateSequence Analysisindels_3waydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way
kernel_canonical_correlation_analysis1.0.0rpyTo updateKernel Canonical Correlation AnalysisTo updateStatisticskernel_canonical_correlation_analysisdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis
kernel_principal_component_analysis1.0.0rpyTo updateKernel Principal Component AnalysisTo updateStatisticskernel_principal_component_analysisdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis
lastz_paired_reads1.1.11.04.22lastzTo updateGalaxy wrapper for the Lastz alignment tool on paired readsTo updateNext Gen Mapperslastz_paired_readsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads
lda_analysis1.0.1RTo updatePerform Linear Discriminant AnalysisTo updateGraphics, Statisticslda_analysisdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis
linear_regression1.0.1RTo updatePerform Linear RegressionTo updateStatisticslinear_regressiondevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression
logistic_regression_vif1.0.1numpyTo updatePerform Logistic Regression with vifTo updateSequence Analysis, Variant Analysis, Statisticslogistic_regression_vifdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif
maf_cpg_filter1.0.00.10.0bx-pythonTo updateMask CpG/non-CpG sites from MAF fileTo updateSequence Analysis, Variant Analysismaf_cpg_filterdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter
mapping_to_ucsc1.0.0To updateFormat mapping data as UCSC custom trackTo updateVisualization, Convert Formats, Next Gen Mappersmapping_to_ucscdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc
megablast_xml_parser1.0.1pythonTo updateParse blast XML outputTo updateNext Gen Mappers, Convert Formatsmegablast_xml_parserdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser
merge_cols1.0.3pythonTo updateMerge columns together.To updateText Manipulationmerge_colsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols
microsatellite_birthdeath1.0.0To updateIdentify microsatellite births and deathsTo updateSequence Analysismicrosatellite_birthdeathdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath
microsats_alignment_level1.0.0sputnikTo updateExtract Orthologous Microsatellites from pair-wise alignmentsTo updateSequence Analysis, Variant Analysismicrosats_alignment_leveldevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level
microsats_mutability1.1.00.10.0bx-pythonTo updateEstimate microsatellite mutability by specified attributesTo updateSequence Analysis, Variant Analysismicrosats_mutabilitydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability
mine0.0.1MINETo updateMaximal Information-based Nonparametric ExplorationTo updateVariant Analysisminedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/mine
multispecies_orthologous_microsats1.0.0bx-sputnikTo updateExtract orthologous microsatellitesTo updateSequence Analysis, Variant Analysismultispecies_orthologous_microsatsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats
mutate_snp_codon1.0.0To updateMutate Codons with SNPsTo updateVariant Analysismutate_snp_codondevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon
partialr_square1.0.0RTo updateCompute partial R squareTo updateStatisticspartialr_squaredevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square
pearson_correlation1.0.0To updatePearson and apos Correlation between any two numeric columnsTo updateStatisticspearson_correlationdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation
pgsnp2gd_snp1.0.0To updateConvert from pgSnp to gd_snpTo updateVariant Analysispgsnp2gd_snpdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp
pileup_interval1.0.30.10.0bx-pythonTo updatePileup-to-Interval condenses pileup format into ranges of basesTo updateSAMpileup_intervaldevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval
pileup_parser1.0.2perlTo updateFilter pileup on coverage and SNPsTo updatehttps://github.com/galaxyproject/tools-devteam/SAMpileup_parserdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser
plot_from_lda1.0.1RTo updateDraw ROC plot on "Perform LDA" outputTo updateGraphics, Statisticsplot_from_ldadevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda
principal_component_analysis1.0.2rpyTo updatePrincipal Component AnalysisTo updateStatisticsprincipal_component_analysisdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis
quality_filter1.0.10.10.0bx-pythonTo updateFilter nucleotides based on quality scoresTo updateSequence Analysis, Variant Analysisquality_filterdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter
rcve1.0.0RTo updateCompute RCVETo updateSequence Analysis, Variant Analysisrcvedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve
remove_beginning1.0.0To updateRemove lines from the beginning of a file.To updateText Manipulationremove_beginningdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning
rmap1.0.02.1rmapTo updateRMAP for Solexa Short Reads AlignmentTo updateNext Gen Mappersrmapdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap
rmapq1.0.02.1rmapTo updateRMAPQ for Solexa Short Reads Alignment with Quality ScoresTo updateNext Gen Mappersrmapqdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq
sam2interval1.0.2pythonTo updateConvert SAM to interval.To updateSAMsam2intervaldevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval
sam_bitwise_flag_filter1.0.1pythonTo updateFilter SAM on bitwise flag valuesTo updateSAMsam_bitwise_flag_filterdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter
scatterplot1.0.3numpyTo updateScatterplot of two numeric columnsTo updateGraphics, Statisticsscatterplotdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot
short_reads_figure_high_quality_length1.0.0rpyTo updateHistogram of high quality score readsTo updateSequence Analysis, Graphicsshort_reads_figure_high_quality_lengthdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length
short_reads_figure_score1.0.2fontconfigTo updateBuild base quality distributionTo updateSequence Analysis, Graphicsshort_reads_figure_scoredevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score
short_reads_trim_seq1.0.0To updateSelect high quality segmentsTo updateFastq Manipulationshort_reads_trim_seqdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq
show_beginning1.0.0To updateSelect lines from the beginning of a file.To updateText Manipulationshow_beginningdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning
show_tail1.0.0To updateSelect lines from the end of a file.To updateText Manipulationshow_taildevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail
sicer1.11.1SICERUp-to-dateStatistical approach for the Identification of ChIP-Enriched RegionsUp-to-datehttps://home.gwu.edu/~wpeng/Software.htmChIP-seqsicerdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer
split_paired_reads1.0.0To updateSplit paired end readsTo updateFastq Manipulationsplit_paired_readsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads
substitution_rates1.0.0To updateEstimate substitution rates for non-coding regionsTo updateSequence Analysis, Variant Analysissubstitution_ratesdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates
substitutions1.0.10.10.0bx-pythonTo updateFetch substitutions from pairwise alignmentsTo updateSequence Analysis, Variant Analysissubstitutionsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions
t_test_two_samples1.0.1RTo updateT Test for Two SamplesTo updateStatisticst_test_two_samplesdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples
table_annovar0.2annovarTo updateAnnotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filteredTo updateVariant Analysistable_annovardevteamNonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar
tabular_to_fasta1.1.1pythonTo updateTabular-to-FASTATo updateConvert Formatstabular_to_fastadevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta
tophat1.5.01.18samtoolsTo updateTophat for IlluminaTo updateRNA, Next Gen Mapperstophatdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat
tophat22.1.12.5.2bowtie2To updateTophat - fast splice junction mapper for RNA-Seq readsTo updatehttp://ccb.jhu.edu/software/tophat/index.shtmlRNA, Next Gen Mapperstophat2devteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2
tophat_fusion_post0.1blast+To updateWrapper for Tophat-Fusion post stepTo updateTranscriptomicstophat_fusion_postdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post
trimmer0.0.1To updateTrim leading or trailing characters.To updateText Manipulationtrimmerdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer
ucsc_custom_track1.0.1pythonTo updateBuild custom track for UCSC genome browserTo updateSequence Analysisucsc_custom_trackdevteamhttps://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track
varscan_version_22.4.22.4.6varscanTo updateVarScan wrapperTo updatehttps://dkoboldt.github.io/varscan/Variant Analysisvarscan_version_2devteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2
vcf2pgsnp1.0.0To updateVCF to pgSnpTo updateVariant Analysisvcf2pgsnpdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp
vcf_annotate1.0.0To updateAnnotate a VCF file (dbSNP, hapmap)To updateVariant Analysisvcf_annotatedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate
vcf_extract1.0.0To updateExtract reads from a specified regionTo updateVariant Analysisvcf_extractdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract
vcf_filter1.0.0To updateFilter a VCF fileTo updateVariant Analysisvcf_filterdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter
vcf_intersect1.0.0To updateGenerate the intersection of two VCF filesTo updateVariant Analysisvcf_intersectdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect
weightedaverage1.0.11.1.0galaxy-opsTo updateAssign weighted-average of the values of features overlapping an intervalTo updateSequence Analysis, Variant Analysisweightedaveragedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage
windowsplitter1.0.10.10.0bx-pythonTo updateMake windowsTo updateSequence Analysis, Variant Analysiswindowsplitterdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter
xy_plot1.0.2r-baseTo updatePlotting tool for multiple series and graph typesTo updateGraphics, Statisticsxy_plotdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot
basecoverage1.0.00.10.0bx-pythonTo updateBase Coverage of all intervalsTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationsbasecoveragedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage
cluster1.0.00.10.0bx-pythonTo updateCluster the intervals of a datasetTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationsclusterdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster
complement1.0.00.10.0bx-pythonTo updateComplement intervals of a datasetTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationscomplementdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement
concat1.0.10.10.0bx-pythonTo updateConcatenate two bed filesTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationsconcatdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat
coverage1.0.00.10.0bx-pythonTo updateCoverage of a set of intervals on second set of intervalsTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationscoveragedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage
flanking_features4.0.10.10.0bx-pythonTo updateFetch closest non-overlapping feature for every intervalTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationsflanking_featuresdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features
get_flanks1.0.00.10.0bx-pythonTo updateGet flanks returns flanking region/s for every geneTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationsget_flanksdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks
intersect1.0.00.10.0bx-pythonTo updateIntersect the intervals of two datasetsTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationsintersectdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect
join1.0.00.10.0bx-pythonTo updateJoin the intervals of two datasets side-by-sideTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationsjoindevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join
merge1.0.00.10.0bx-pythonTo updateMerge the overlapping intervals of a datasetTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationsmergedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge
subtract1.0.00.10.0bx-pythonTo updateSubtract the intervals of two datasetsTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationssubtractdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract
subtract_query0.10.10.0bx-pythonTo updateSubtract Whole Dataset from another datasetTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationssubtract_querydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query
tables_arithmetic_operations1.0.0perlTo updateArithmetic Operations on tablesTo updatehttps://github.com/galaxyproject/gopsGenomic Interval Operationstables_arithmetic_operationsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations
hgv_fundo1.0.0To updateFunDO human genes associated with disease termsTo updateSequence Analysishgv_fundodevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo
hgv_hilbertvis1.0.0RTo updateHVIS visualization of genomic data with the Hilbert curveTo updatehttps://www.ebi.ac.uk/huber-srv/hilbert/Graphics, Visualizationhgv_hilbertvisdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis
snpfreq1.0.1RTo updatesnpFreq significant SNPs in case-control dataTo updateVariant Analysis, Statisticssnpfreqdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq
find_diag_hits1.0.00.9.0taxonomyTo updateFind diagnostic hitsTo updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicsfind_diag_hitsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits
gi2taxonomy1.1.10.9.0taxonomyTo updateFetch taxonomic representationTo updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicsgi2taxonomydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy
kraken2tax1.2+galaxy0gawkTo updateConvert Kraken output to Galaxy taxonomy data.To updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicskraken2taxdevteamhttps://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/
lca_wrapper1.0.10.9.0taxonomyTo updateFind lowest diagnostic rankTo updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicslca_wrapperdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper
poisson2test1.0.00.9.0taxonomyTo updatePoisson two-sample testTo updatehttps://bitbucket.org/natefoo/taxonomyStatistics, Metagenomicspoisson2testdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test
t2ps1.0.00.9.0taxonomyTo updateDraw phylogenyTo updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicst2psdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps
t2t_report1.0.00.9.0taxonomyTo updateSummarize taxonomyTo updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicst2t_reportdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report
vcftools_annotate0.1echoTo updateAnnotate VCF using custom/user-defined annotationsTo updatehttps://vcftools.github.io/Variant Analysisvcftools_annotatedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate
vcftools_compare0.11.11tabixTo updateCompare VCF files to get overlap and uniqueness statisticsTo updatehttps://vcftools.github.io/Variant Analysisvcftools_comparedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare
vcftools_consensus0.1.111.18samtoolsTo updateApply VCF variants to a fasta file to create consensus sequenceTo updatehttps://vcftools.github.io/Variant Analysisvcftools_consensusdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus
vcftools_isec0.1.11.11tabixTo updateIntersect multiple VCF datasetsTo updatehttps://vcftools.github.io/Variant Analysisvcftools_isecdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec
vcftools_merge0.1.111.11tabixTo updateMerge multiple VCF datasets into a single datasetTo updatehttps://vcftools.github.io/Variant Analysisvcftools_mergedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge
vcftools_slice0.1echoTo updateSubset VCF dataset by genomic regionsTo updatehttps://vcftools.github.io/Variant Analysisvcftools_slicedevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice
vcftools_subset0.11.11tabixTo updateSelect samples from a VCF datasetTo updatehttps://vcftools.github.io/Variant Analysisvcftools_subsetdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset
10x_bamtofastq1.4.11.4.110x_bamtofastqUp-to-dateConverts 10x Genomics BAM to FASTQUp-to-datehttps://github.com/10XGenomics/bamtofastqConvert Formats10x_bamtofastqbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq
AggregateAlignments0.6.00.6.0graphclust-wrappersUp-to-dateAggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.Up-to-dateRNAgraphclust_aggregate_alignmentsrnateamhttps://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments
AlignCluster0.10.6.0graphclust-wrappersTo updateAlign predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.To updateRNAgraphclust_align_clusterrnateamhttps://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster
CMFinder0.40.6.0graphclust-wrappersTo updateDetermines consensus motives for sequences.To updateRNAgraphclust_cmfinderrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder
CollectResults0.50.6.0graphclust-wrappersTo updatePost-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.To updateRNAgraphclust_postprocessingrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults
CollectResultsNoAlign0.50.6.0graphclust-wrappersTo updateRedundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.To updateRNAgraphclust_postprocessing_no_alignrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign
GSPAN0.40.6.0graphclust-wrappersTo updateSecond step of GraphClustTo updateRNAgraphclust_fasta_to_gspanrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN
LocARNAGraphClust0.40.6.0graphclust-wrappersTo updateMLocARNA computes a multiple sequence-structure alignment of RNA sequences.To updateRNAgraphclust_mlocarnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust
NSPDK9.2.3.10.6.0graphclust-wrappersTo updateProduces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.To updateRNAgraphclust_nspdkrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK
Plotting0.4seabornTo updatePlotting results for GraphClustTo updateRNAgraphclust_motif_finder_plotrnateamhttps://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting
PrepareForMlocarna0.40.6.0graphclust-wrappersTo updateThis tool prepares files for locarna step.To updateRNAgraphclust_prepocessing_for_mlocarnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna
Preprocessing0.50.6.0graphclust-wrappersTo updatePreprocessing input for GraphClustTo updateRNAgraphclust_preprocessingrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/GraphClust
Structure_GSPAN0.40.6.0graphclust-wrappersTo updateConvert RNA structure to GSPAN graphsTo updateRNAstructure_to_gspanrnateamhttps://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN
agat1.2.01.2.0agatUp-to-dateagatAGATData handling, Genome annotationGenomicsGTF/GFF analysis toolkitAnother Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.Up-to-datehttps://github.com/NBISweden/AGATConvert Formats, Statistics, Fasta Manipulationagatbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/agat
antismash6.1.16.1.1antismashUp-to-dateantismashantiSMASHSequence clustering, Gene prediction, Differential gene expression analysisMolecular interactions, pathways and networks, Gene and protein familiesAntismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clustersRapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.Up-to-datehttps://antismash.secondarymetabolites.orgSequence Analysisantismashbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash
atactk_trim_adapters0.1.60.1.9atactkTo updateTrim adapters from paired-end HTS reads.To updatehttps://github.com/ParkerLab/atactk/Fastq Manipulationatactk_trim_adaptersrnateamhttps://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters
augustus3.1.03.5.0augustusTo updateAUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.To updatehttp://bioinf.uni-greifswald.de/augustus/Sequence Analysisaugustusbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/augustus
bamhash1.11.1bamhashUp-to-dateHash BAM and FASTQ files to verify data integrityUp-to-datehttps://github.com/DecodeGenetics/BamHashSequence Analysisbamhashbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/bamhash
barcode_collapse0.1.00.22.0pysamTo updatePaired End randomer aware duplicate removal algorithmTo updatehttps://github.com/YeoLab/gscriptsRNA, Sequence Analysisbarcode_collapsernateamhttps://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse
bigwig_to_bedgraph0.1.0ucsc_toolsTo updateConvert from bigWig to bedGraph formatTo updateConvert Formatsbigwig_to_bedgraphbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph
bionano3.7.0To updateBionano Solve is a set of tools for analyzing Bionano dataTo updatehttps://bionanogenomics.com/Assemblybionanobgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/bionano
bismark0.22.10.24.2bismarkTo updateA tool to map bisulfite converted sequence reads and determine cytosine methylation statesTo updatehttps://www.bioinformatics.babraham.ac.uk/projects/bismark/Sequence Analysis, Next Gen Mappersbismarkbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/bismark
blobtoolkit4.0.7To updateIdentification and isolation non-target data in draft and publicly available genome assemblies.To updatehttps://blobtoolkit.genomehubs.org/Sequence Analysis, Assemblyblobtoolkitbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit
blockbuster0.1.20.0.1.1blockbusterTo updateBlockbuster detects blocks of overlapping reads using a gaussian-distribution approach.To updatehttp://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.htmlRNA, Sequence Analysisblockbusterrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/blockbuster
canu2.22.2canuUp-to-datecanuCANUDe-novo assemblyGenomicsCanu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.Up-to-datehttps://github.com/marbl/canucanubgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/canu
cellprofilerTo updatecellProfiler wrapperTo updateImagingcellprofilerbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools
cellprofiler_v44.2.1To updatecellProfiler4 wrapperTo updateImagingcellprofiler4bgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools
chipseeker1.32.01.36.0bioconductor-chipseekerTo updateA tool for ChIP peak annotation and visualizationTo updatehttps://bioconductor.org/packages/release/bioc/html/ChIPseeker.htmlChIP-seq, Genome annotationchipseekerrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/chipseeker
circexplorer1.1.9.01.1.10circexplorerTo updateA combined strategy to identify circular RNAs (circRNAs and ciRNAs)To updatehttps://github.com/YangLab/CIRCexplorerSequence Analysis, RNAcircexplorerbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/circexplorer
combine_metaphlan_humann0.3.0pythonTo updateCombine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundancesTo updateMetagenomicscombine_metaphlan2_humann2bebatuthttps://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2
compare_humann2_output0.2.0To updateCompare outputs of HUMAnN2 for several samples and extract similar and specific informationTo updateMetagenomicscompare_humann2_outputbebatuthttps://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output
cpat3.0.43.0.4cpatUp-to-dateCoding-potential assessment tool using an alignment-free logistic regression model.Up-to-datehttps://github.com/liguowang/cpatTranscriptomicscpatbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/cpat
crt1.2.01.2crisper_recognition_toolTo updateCRISPR Recognition ToolTo updateSequence Analysiscrispr_recognition_toolbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/crt
diff3.7diffutilsTo updateGNU diff tool that calculates the differences between two files.To updatehttp://www.gnu.org/software/diffutils/Text Manipulationdiffbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/diff
diffbindTo updateDiffbind provides functions for processing ChIP-Seq data.To updatehttp://bioconductor.org/packages/release/bioc/html/DiffBind.htmlChIP-seqdiffbindbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/diffbind
edta2.1.0edtaTo updateedtaThe Extensive de novo TE Annotator (EDTA)De-novo assembly, Deisotoping, Genome annotationWorkflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organismsThe EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations.The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.To updatehttps://github.com/oushujun/EDTAVariant Analysisedtabgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/edta
epicseg@VERSION_STRING@1.0epicsegTo updateEpiCSeg is a tool for conducting chromatin segmentation.To updatehttps://github.com/lamortenera/epicsegEpigeneticsepicsegrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/epicseg
fastq_info0.25.10.25.2fastq_utilsTo updateFASTQ info allows to validate single or paired fastq filesTo updatehttps://github.com/nunofonseca/fastq_utilsFastq Manipulationfastq_infobgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/fastq_info
file_manipulation0.4pythonTo updateThis tool returns all unique lines from a tab-separated file.To updatehttps://github.com/bgruening/galaxytools/tree/master/tools/file_manipulationText Manipulationuniquebgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation
find_subsequences0.31.70biopythonTo updateTo updatefind_subsequencesbgruening
flye2.9.12.9.2flyeTo updateAssembly of long and error-prone reads.To updatehttps://github.com/fenderglass/Flye/Assemblyflyebgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/flye
footprint1.0.01.0.1footprintTo updateFind transcription factor footprintsTo updatehttps://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/Epigeneticsfootprintrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/footprint
format_cd_hit_output1.0.0+galaxy1To updateFormat CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping fileTo updateFasta Manipulationformat_cd_hit_outputbebatuthttps://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/
format_metaphlan2_output0.2.0To updateFormat MetaPhlAn2 output to extract abundance at different taxonomic levelsTo updateMetagenomicsformat_metaphlan2_outputbebatuthttps://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/
gfastats1.3.61.3.6gfastatsUp-to-dategfastatsgfastatsData handlingComputational biologyTool for generating sequence statistics and simultaneous genome assembly file manipulation.gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.Up-to-datehttps://github.com/vgl-hub/gfastatsSequence Analysisgfastatsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/gfastats
glimmer_hmmTo updateGlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)To updatehttps://ccb.jhu.edu/software/glimmerhmm/Sequence Analysisglimmer_hmmbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm
gotohscan1.3.01.3gotohscanTo updateFind subsequences in dbTo updateSequence Analysisgotohscanrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/gotohscan
graph_converter0.1.0To updateConvert between different graph formatsTo updateConvert Formatsgraph_converterbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/graph_converter
graphclust0.1GraphClustTo updateGraphClust can be used for structural clustering of RNA sequences.To updatehttp://www.bioinf.uni-freiburg.de/Software/GraphClust/RNAgraphclustbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/graphclust
graphmap0.5.20.6.3graphmapTo updateMapper for long, error-prone reads.To updatehttps://github.com/isovic/graphmap/Assemblygraphmapbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/graphmap
hclust20.991.0.0hclust2To updatePlots heatmapsTo updatehttps://bitbucket.org/nsegata/hclust2/Data Visualizationhclust2rnateamhttps://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2
hicup0.9.2To updateThe HiCUP-Pipeline from the Bioinformatics Babraham Institute.To updatehttps://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.htmlEpigeneticshicupbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/hicup
hifiasm0.19.70.19.7hifiasmUp-to-dateA fast haplotype-resolved de novo assemblerUp-to-datehttps://github.com/chhylp123/hifiasmAssemblyhifiasmbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/hifiasm
homerTo updateSoftware for motif discovery and next generation sequencing analysis.To updatehttp://homer.salk.edu/homer/Sequence Analysishomerbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/homer
illumina_methylation_analyser0.1RscriptTo updateMethylation analyzer for Illumina 450k DNA emthylation microarraysTo updatehttps://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyserSequence Analysisillumina_methylation_analyserbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser
graphicsmagick1.3.311.3.26graphicsmagickTo updateContains tools based on GraphicsMagickTo updatehttp://www.graphicsmagick.orgImaginggraphicsmagickbgrueninghttps://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/
imagej2To updateImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.To updatehttp://fiji.scImagingimagej2imgteamhttps://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2
instagraal0.1.6To updateinstagraalinstaGRAALGenome assembly, Mapping assembly, Genetic mapping, ScaffoldingSequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sitesLarge genome reassembly based on Hi-C dataChromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)To updatehttps://github.com/koszullab/instaGRAALAssemblyinstagraalbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/instagraal
iprscan5To updateInterproscan queries the interpro database and provides annotations.To updatehttp://www.ebi.ac.uk/Tools/pfa/iprscan5/Sequence Analysisiprscan5bgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/iprscan5
itsx1.1.31.1.3itsxUp-to-dateITSxITSxSequence feature detectionFunctional, regulatory and non-coding RNA, MicrobiologyITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.Up-to-datehttps://microbiology.se/software/itsx/Metagenomicsitsxbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/itsx
jupyter_job0.0.1To updateRun jupyter notebook script in GalaxyTo updateMachine Learningrun_jupyter_jobbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job
labels1.0.5.0labelsTo updateremaps and annotates alignmentsTo updatehttps://github.com/bgruening/galaxytools/tree/master/tools/labelsSequence Analysislabelsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/labels
lighter1.01.1.2lighterTo updateLighter is a kmer-based error correction method for whole genome sequencing dataTo updateSequence Analysis, Fasta Manipulationlighterbgrueninghttps://github.com/mourisl/Lighter
mafft7.5087.520mafftTo updateMAFFTMAFFTMultiple sequence alignmentSequence analysisMultiple alignment program for amino acid or nucleotide sequencesMAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.To updateRNAmafftrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/mafft
mcl14.13722.282mclTo updateMarkov Cluster AlgorithmTo updatehttp://micans.org/mcl/Sequence Analysis, Metagenomicsmclbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/mcl
methtools0.1.1methtoolsTo updatetools for methylation analysisTo updatehttps://github.com/bgruening/galaxytools/tree/master/tools/methtoolsSequence Analysismethtoolsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/methtools
methyldackel0.5.20.6.1methyldackelTo updateA tool for processing bisulfite sequencing alignmentsTo updatehttps://github.com/dpryan79/MethylDackelSequence Analysispileomethbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/methyldackel
methylkit0.99.21.26.0bioconductor-methylkitTo updateA method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.To updatehttp://bioconductor.org/packages/release/bioc/html/methylKit.htmlEpigeneticsmethylkitrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/methylkit
metilene0.2.6.10.2.8metileneTo updateDifferential DNA methylation callingTo updateRNA, Statisticsmetilenernateamhttps://github.com/bgruening/galaxytools/tree/master/tools/metilene
miclip1.2.0RscriptTo updateIdentification of binding sites in CLIP-Seq data.To updatehttps://cran.r-project.org/src/contrib/Archive/MiClip/Sequence Analysismiclipbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/miclip
minced0.2.00.4.2mincedTo updateMinCED - Mining CRISPRs in Environmental DatasetsTo updatehttp://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_READMESequence Analysismincedbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/minced
minipolish0.1.30.1.3minipolishUp-to-dateminipolishminipolishLocalised reassemblySequence assemblyPolishing miniasm assembliesA tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.Up-to-datehttps://github.com/rrwick/MinipolishSequence Analysisminipolishbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/minipolish
mitohifi3To updateAssembly mitogenomes from Pacbio HiFi read.To updatehttps://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2Assemblymitohifibgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/mitohifi
molecule2gspan0.22.3.90dev7d621d9openbabelTo updateconverterTo updatehttps://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspanConvert Formatsmolecule_to_gspanbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan
music_deconvolution0.1.10.1.1music-deconvolutionUp-to-dateMulti-subject Single Cell deconvolution (MuSiC)Up-to-datehttps://github.com/xuranw/MuSiCTranscriptomicsmusicbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/music/
nanopolish0.13.20.14.0nanopolishTo updateNanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.To updatehttps://github.com/jts/nanopolishnanopolishbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/nanopolish
netboxr1.6.01.9.0bioconductor-netboxrTo updatenetboxr enables automated discovery of biological process modules by network analysisTo updateSystems Biologynetboxrbgruening
nextdenovo2.5.02.5.2nextdenovoTo updatenextdenovoNextDenovoDe-novo assembly, Genome assemblySequencing, Sequence assemblyString graph-based de novo assembler for long readsNextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages.To updatehttps://github.com/Nextomics/NextDenovoAssemblynextdenovobgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo
nucleosome_prediction3.03.0nucleosome_predictionUp-to-datePrediction of Nucleosomes Positions on the GenomeUp-to-datehttps://genie.weizmann.ac.il/software/nucleo_exe.htmlSequence Analysisnucleosome_predictionbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction
numeric_clustering0.9anacondaTo updateClustering tool for numberic valuesTo updatehttp://scikit-learn.org/stable/index.htmlStatisticsnumeric_clusteringbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering
openms2.1.03.1.0openmsTo updateOpenMS in version 2.1.To updateProteomicsopenmsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/openms
pandas_rolling_window0.1numpyTo updateRolling window calculationsTo updatehttps://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.htmlStatisticspandas_rolling_windowbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window
peakachu0.2.0+galaxy10.2.0peakachuTo updatePEAKachu is a peak-caller for CLIP- and RIP-Seq dataTo updateSequence Analysis, RNApeakachurnateamhttps://github.com/tbischler/PEAKachu
perf5.11.0perfTo updatesuitable for boolean classification problemsTo updatehttp://osmot.cs.cornell.edu/kddcup/software.htmlstats_perf_toolbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/perf
pfamscan1.61.6pfam_scanUp-to-datepfamscanPfamScanProtein sequence analysisSequence analysisSearch a FASTA sequence against a library of Pfam HMM.This tool is used to search a FASTA sequence against a library of Pfam HMM.Up-to-datehttp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/Sequence Analysispfamscanbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/pfamscan
pg_toolspostgresqlTo updatetool suite for dealing with Postgresql databases from Galaxy's historyTo updatehttps://www.postgresql.orgData Export, Data Sourcepgtoolsbgrueninghttps://github.com/bgruening/galaxytools/tools/pgtools
pharmcatTo updatePharmacogenomics Clinical Annotation ToolTo updatehttps://pharmcat.org/Variant Analysispharmcatbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/pharmcat
piranha1.2.1.01.2.1piranhaTo updatePiranha is a peak-caller for CLIP- and RIP-Seq dataTo updateSequence Analysis, RNApiranharnateamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha
platypus0.0.11platypusTo updateefficient and accurate variant-detection in high-throughput sequencing dataTo updatehttp://www.well.ox.ac.uk/platypusSequence Analysisplatypusbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/platypus
plotly_ml_performance_plots0.2pandasTo updateperformance plots for machine learning problemsTo updatehttp://scikit-learn.org/stable/modules/classes.html#module-sklearn.metricsVisualizationplotly_ml_performance_plotsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots
plotly_parallel_coordinates_plot0.2pythonTo updateparallel coordinates plot produced with plotlyTo updatehttps://plot.ly/python/parallel-coordinates-plot/Visualizationplotly_parallel_coordinates_plotbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot
plotly_regression_performance_plots0.1pythonTo updateperformance plots for regression problemsTo updatehttp://scikit-learn.org/stable/supervised_learning.html#supervised-learningVisualizationplotly_regression_performance_plotsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots
protease_prediction0.92.0edenTo updateThis tool can learn the cleavage specificity of a given class of proteases.To updatehttps://github.com/fabriziocosta/edenSequence Analysis, Proteomicsprotease_predictionbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction
protein_properties0.2.01.70biopythonTo updateCalculation of various properties from given protein sequencesTo updateSequence Analysisprotein_propertiesbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/protein_properties
improviser1.1.0.1To updateVisualisation of PepXML filesTo updatehttp://www.improviser.uni-freiburg.de/Proteomicsproteomics_improviserbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser
racon1.5.01.5.0raconUp-to-dateConsensus module for raw de novo DNA assembly of long uncorrected reads.Up-to-datehttps://github.com/isovic/raconSequence Analysisraconbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/racon
repeat_masker0.1.24.1.5RepeatMaskerTo updateRepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.To updatehttp://www.repeatmasker.org/Sequence Analysisrepeat_maskerbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker
replaceColumn0.2To updateA tool to replace all column entries of a file given by values of a key-value file.To updateText Manipulationreplace_column_by_key_value_filebgrueninghttps://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn
rest_tool0.1.0To updateThis tool fetches data from pubchem via the PubChem REST API.To updatehttps://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.htmlData Sourcepubchem_rest_toolbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/rest_tool
antarna1.12.0.1.2antarnaTo updateantaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .To updateRNAantarnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/
aresite20.1.2pythonTo updateAREsite2 REST InterfaceTo updatehttp://rna.tbi.univie.ac.at/AREsiteRNA, Data Source, Sequence Analysisaresite2rnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2
blockclust1.1.01.1.0blockclustUp-to-dateBlockClust detects transcripts with similar processing patterns.Up-to-datehttps://github.com/bgruening/galaxytools/tree/master/workflows/blockclustRNAblockclustrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust
cmsearch_deoverlap0.08+galaxy0perlTo updateremoves lower scoring overlaps from cmsearch results.To updatehttps://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.plRNAcmsearch_deoverlaprnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap
cmv1.0.81.0.8cmvUp-to-datecmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.Up-to-datehttps://github.com/eggzilla/cmvRNAcmvrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv
cofold2.0.4.02.0.4cofoldTo updateCofold predicts RNA secondary structures that takes co-transcriptional folding into account.To updatehttp://www.e-rna.org/cofold/RNAcofoldrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold
compalignp1.01.0compalignpUp-to-dateCompute fractional identity between trusted alignment and test alignmentUp-to-dateRNA, Sequence Analysiscompalignprnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/
coprarna2.1.12.1.4coprarnaTo updateTarget prediction for prokaryotic trans-acting small RNAsTo updatehttps://github.com/PatrickRWright/CopraRNARNA, Sequence Analysiscoprarnarnateamhttps://github.com/PatrickRWright/CopraRNA
dewseq0.1.0+galaxy0pythonTo updateDEWSeq is a sliding window based peak caller for eCLIP/iCLIP dataTo updatehttps://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpersSequence Analysis, RNA, CLIP-seqdewseqrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq
dorina1.0To updatedata source for RNA interactions in post-transcriptional regulationTo updateRNA, Data Sourcedorinarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/
dot2ct5.7.a6.3rnastructureTo updateDot-Bracket to Connect Table (CT)To updateSequence Analysis, RNAdot2ctrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct
dotknot1.3.1vienna_rnaTo updateDotKnot is a heuristic method for pseudoknot prediction in a given RNA sequenceTo updatehttp://dotknot.csse.uwa.edu.au/RNA, Proteomicsdotknotbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot
exparna1.0.11.0.1exparnaUp-to-dateExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.Up-to-datehttp://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jspRNAexparnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna
graphprot1.1.7+galaxy11.1.7graphprotTo updateGraphProt models binding preferences of RNA-binding proteins.To updatehttps://github.com/dmaticzka/GraphProtSequence Analysis, RNA, CLIP-seqgraphprotrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot
htseq-clip0.1.0+galaxy02.19.0b0htseq-clipTo updatehtseq-clip is a toolset for the analysis of eCLIP/iCLIP datasetsTo updatehttps://github.com/EMBL-Hentze-group/htseq-clipSequence Analysis, RNA, CLIP-seqhtseq_cliprnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip
infernal1.1.41.1.4infernalUp-to-dateinfernalInfernalNucleic acid feature detectionSequence sites, features and motifsInfernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.Up-to-datehttp://infernal.janelia.org/RNAinfernalbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/infernal
infornaTo updateINFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.To updatehttp://rna.informatik.uni-freiburg.de/INFORNA/Input.jspRNAinfornarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna
intarna3.3.23.3.2intarnaUp-to-dateEfficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.Up-to-datehttps://github.com/BackofenLab/IntaRNARNAintarnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna
kinwalkerTo updateKinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.To updatehttp://www.bioinf.uni-leipzig.de/Software/Kinwalker/RNAkinwalkerrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker
locarna1.9.2.32.0.0locarnaTo updateLocARNA - A suite for multiple alignment and folding of RNAsTo updatehttp://www.bioinf.uni-freiburg.de/Software/LocARNA/RNAlocarnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna
mea0.6.4.10.6.4meaTo updateMaximum expected accuracy predictionTo updatehttp://www.bioinf.uni-leipzig.de/Software/meaRNAmearnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea
mqc1.91.10mqcTo updateRibosome profiling mapping quality control toolTo updatehttps://github.com/Biobix/mQCSequence Analysismqcrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/
nastiseq1.01.0r-nastiseqUp-to-dateA method to identify cis-NATs using ssRNA-seqUp-to-datehttps://ohlerlab.mdc-berlin.de/software/NASTIseq_104/RNAnastiseqrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq
paralyzer1.51.5paralyzerUp-to-dateA method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.Up-to-datehttps://ohlerlab.mdc-berlin.de/software/PARalyzer_85/RNAparalyzerrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer
pipmir0.1.01.1pipmirTo updateA method to identify novel plant miRNA.To updatehttps://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/RNApipmirrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir
rRNA0.1hmmsearch3.0To updateIdentification of ribosomal RNA genes in metagenomic fragments.To updatehttp://weizhong-lab.ucsd.edu/meta_rna/RNArrnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rRNA
rcas1.5.41.26.0bioconductor-rcasTo updateRCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experimentsTo updatehttps://github.com/BIMSBbioinfo/RCASRNArcasrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/
reago1.11.1reagoUp-to-dateReago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.Up-to-datehttps://github.com/chengyuan/reago-1.1Metagenomics, RNAreagornateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago
remurna1.0.01.0remurnaTo updateremuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA ConformationTo updatehttps://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurnaRNAremurnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna
ribotaper1.3.1a1.3.1ribotaperTo updateribotaperRiboTaperGene expression profilingFunctional genomicsA method for defining traslated ORFs using Ribosome Profiling data.New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.To updatehttps://ohlerlab.mdc-berlin.de/software/RiboTaper_126/RNAribotaperrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/
rna_shapes3.3.0@EXECUTABLE@To updateCompute secondary structures of RNATo updateRNArnashapesrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes
rnabob2.2.1.02.2.1rnabobTo updateFast pattern searching for RNA structural motifsTo updatehttp://eddylab.org/software.htmlRNArnabobrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob
rnacode0.3.20.3rnacodeTo updateAnalyze the protein coding potential in MSATo updateRNArnacodernateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode
rnacommender0.1.13.5samTo updateRNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.To updatehttps://github.com/gianlucacorrado/RNAcommenderRNArnacommenderrnateamhttps://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender
rnalien1.3.61.8.0rnalienTo updateRNAlien unsupervized RNA family model constructionTo updatehttp://rna.tbi.univie.ac.at/rnalien/RNA, Sequence Analysisrnalienrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien
rnasnp1.2.01.2rnasnpTo updateRNAsnp Efficient detection of local RNA secondary structure changes induced by SNPsTo updatehttp://rth.dk/resources/rnasnp/RNArnasnprnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rnasnp
rnaz2.1.12.1.1rnazUp-to-dateRNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.Up-to-datehttps://www.tbi.univie.ac.at/~wash/RNAz/RNArnazbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz
selectsequencesfrommsa1.0.51.0.5selectsequencesfrommsaUp-to-dateSelectSequences - selects representative entries from a multiple sequence alignment in clustal formatUp-to-datehttps://github.com/eggzilla/SelectSequencesRNA, Sequence Analysisselectsequencesfrommsarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa
sortmerna4.3.64.3.6sortmernaUp-to-dateSortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.Up-to-datehttp://bioinfo.lifl.fr/RNA/sortmerna/RNAsortmernarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna
sshmm1.0.71.0.7sshmmUp-to-datessHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq dataUp-to-datehttps://github.molgen.mpg.de/heller/ssHMMSequence Analysis, RNAsshmmrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/
targetfinder1.71.7targetfinderUp-to-datePlant small RNA target prediction toolUp-to-datehttps://github.com/carringtonlab/TargetFinder.gitRNAtargetfinderrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/
trna_prediction0.61.2.41aragornTo updateAragorn predicts tRNA and tmRNA in nucleotide sequences.To updatehttp://mbioserv2.mbioekol.lu.se/ARAGORN/RNAtrna_predictionbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction
vienna_rna2.2.102.6.4viennarnaTo updateViennaRNA - Prediction and comparison of RNA secondary structuresTo updatehttp://www.tbi.univie.ac.at/RNA/RNAviennarnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna
sailfish0.10.1.1bzip2To updateSailfish is a tool for transcript quantification from RNA-seq dataTo updatehttp://www.cs.cmu.edu/~ckingsf/software/sailfish/Sequence Analysis, RNAsailfishbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/sailfish
salmon1.10.11.10.2salmonTo updateSalmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.To updatehttps://github.com/COMBINE-lab/salmonSequence Analysis, RNA, Transcriptomicsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/salmon
sambamba1.0sambambaTo updateSAMBAMBA: process your BAM data faster!To updatehttps://github.com/lomereiter/sambambaSAMsambambarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/sambamba
sed0.0.1sedTo updateManipulate your data with the sed command line tool.To updatehttps://github.com/bgruening/galaxytools/tree/master/tools/sedText Manipulationsed_wrapperbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/sed
segemehl0.2.0.40.3.4segemehlTo updatesegemehl - short read mapping with gapsTo updatehttp://www.bioinf.uni-leipzig.de/Software/segemehl/Next Gen Mapperssegemehlrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/segemehl
sklearn1.0.10.0To updateMachine Learning tool suite from Scikit-learnTo updatehttp://scikit-learn.orgMachine Learning, Statisticssklearnbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/sklearn
splitfasta0.4.01.70biopythonTo updateSplit a multi-sequence fasta file into files containing single sequencesTo updateText Manipulationsplitfastarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/splitfasta
statistics0.3numpyTo updateTool for computing statistical tests.To updatehttps://github.com/bgruening/galaxytools/tree/master/tools/statisticsStatisticsbg_statistical_hypothesis_testingbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/statistics
stress_ng0.12.04stress-ngTo updatestress test a computer system in various selectable waysTo updateWeb Servicesstress_ngbgruening-utilhttps://github.com/ColinIanKing/stress-ng
add_line_to_file0.1.08.25coreutilsTo updateAdds a text line to the beginning or end of a file.To updateText Manipulationadd_line_to_filebgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file
column_arrange_by_header0.2To updateColumn arrange by header nameTo updateText Manipulationcolumn_arrange_by_headerbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header
join_files_on_column_fuzzy1.0.1pythonTo updateJoin two files on a common column, allowing a certain difference.To updateText Manipulationjoin_files_on_column_fuzzybgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy
split_file_on_column0.6gawkTo updateSplit a file on a specific column.To updateText Manipulationsplit_file_on_columnbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column
split_file_to_collection0.5.0pythonTo updateSplit tabular, MGF, FASTA, or FASTQ files to a dataset collection.To updateText Manipulationsplit_file_to_collectionbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection
text_processing0.1.18.25coreutilsTo updateHigh performance text processing tools using the GNU coreutils, sed, awk and friends.To updatehttps://www.gnu.org/software/Text Manipulationtext_processingbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing
tgsgapcloser1.0.31.2.1tgsgapcloserTo updateTGS-GapCloserTGS-GapCloserGenome assembly, Read mapping, Scaffolding, Localised reassemblySequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, MappingTGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.To updatehttps://github.com/BGI-Qingdao/TGS-GapCloserAssemblytgsgapcloserbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser
tool_recommendation_model0.0.5pythonTo updateCreate model to recommend toolsTo updatehttps://github.com/bgruening/galaxytoolsMachine Learningcreate_tool_recommendation_modelbgrueninghttps://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model
trim_galore0.6.70.6.10trim-galoreTo updatetrim_galoreTrim GaloreSequence trimmingSequence analysisTrim Galore adaptive quality and adapter trimmerA wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.To updatehttp://www.bioinformatics.babraham.ac.uk/projects/trim_galore/Sequence Analysis, Fastq Manipulationtrim_galorebgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/trim_galore
uniprot_rest_interface0.4requestsTo updateUniProt ID mapping and sequence retrievalTo updatehttps://github.com/jdrudolph/uniprotProteomics, Sequence Analysisuniprot_rest_interfacebgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface
vt0.22015.11.10vtTo updateA tool set for short variant discovery in genetic sequence data.To updateSequence Analysis, Variant Analysisvtbgrueninghttps://github.com/atks/vt
wtdbg2.52.5wtdbgUp-to-datewtdbg2wtdbg2Genome assembly, De-novo assembly, Mapping assembly, k-mer countingSequence assembly, Computer science, InformaticsWTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.Up-to-datehttps://github.com/ruanjue/wtdbg2Assemblywtdbgbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/wtdbg
align_back_trans0.0.101.70biopythonTo updateThread nucleotides onto a protein alignment (back-translation)To updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_transFasta Manipulation, Sequence Analysisalign_back_transpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
chromosome_diagram0.0.31.70biopythonTo updateChromosome Diagrams using BiopythonTo updateGraphics, Sequence Analysis, Visualizationchromosome_diagrampeterjc
clc_assembly_cell0.0.71.18samtoolsTo updateGalaxy wrapper for the CLC Assembly Cell suite from CLCBioTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cellAssembly, Next Gen Mappers, SAMclc_assembly_cellpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell
clinod0.1.01.3clinodTo updateNoD: a Nucleolar localization sequence detector for eukaryotic and viral proteinsTo updatehttp://www.compbio.dundee.ac.uk/www-nod/Sequence Analysisclinodpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/clinod
count_roi_variants0.0.61.18samtoolsTo updateCount sequence variants in region of interest in BAM fileTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variantsAssembly, SAMcount_roi_variantspeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants
coverage_stats0.1.01.18samtoolsTo updateBAM coverage statistics using samtools idxstats and depthTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_statsAssembly, SAMcoverage_statspeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats
effectiveT30.0.201.0.1effectiveT3To updateFind bacterial type III effectors in protein sequencesTo updatehttp://effectors.orgSequence Analysiseffectivet3peterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
fasta_filter_by_id0.0.61.1.5galaxy_sequence_utilsTo updateFilter FASTA sequences by ID (DEPRECATED)To updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_idFasta Manipulation, Sequence Analysis, Text Manipulationfasta_filter_by_idpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id
fastq_filter_by_id0.0.61.1.5galaxy_sequence_utilsTo updateFilter FASTQ sequences by ID (DEPRECATED)To updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_idFastq Manipulation, Sequence Analysis, Text Manipulationfastq_filter_by_idpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id
fastq_pair_names0.0.51.1.5galaxy_sequence_utilsTo updateExtract FASTQ paired read namesTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_namesSequence Analysisfastq_pair_namespeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names
fastq_paired_unpaired0.1.41.1.5galaxy_sequence_utilsTo updateDivide FASTQ file into paired and unpaired readsTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpairedSequence Analysis, Text Manipulationfastq_paired_unpairedpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired
get_orfs_or_cdss0.2.31.70biopythonTo updateSearch nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)To updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdssSequence Analysisget_orfs_or_cdsspeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss
mummer0.0.89.18ghostscriptTo updateDraw dotplots using mummer, mucmer, or promer with mummerplotTo updatehttp://mummer.sourceforge.net/Graphics, Sequence Analysis, Visualizationmummerpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/mummer
nlstradamus0.0.111.8NLStradamusTo updateFind nuclear localization signals (NLSs) in protein sequencesTo updatehttp://www.moseslab.csb.utoronto.ca/NLStradamusFasta Manipulation, Sequence Analysisnlstradamuspeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus
predictnls0.0.9To updatePython reimplementation of predictNLS for GalaxyTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/predictnlsSequence Analysispredictnlspeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls
protein_analysis0.0.13promoterTo updateTMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTbTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysisSequence Analysistmhmm_and_signalppeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis
sample_seqs0.2.51.70biopythonTo updateSub-sample sequences files (e.g. to reduce coverage)To updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqsAssembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysissample_seqspeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs
samtools_depad0.0.51.18samtoolsTo updateRe-align a SAM/BAM file with a padded reference (using samtools depad)To updatehttp://www.htslib.org/Assembly, SAM, Sequence Analysissamtools_depadpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad
samtools_depth0.0.31.18samtoolsTo updateCoverage depth via samtoolsTo updatehttp://www.htslib.org/Assembly, Sequence Analysis, SAMsamtools_depthpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth
samtools_idxstats0.0.61.18samtoolsTo updateBAM mapping statistics (using samtools idxstats)To updatehttp://www.htslib.org/Assembly, Next Gen Mappers, SAMsamtools_idxstatspeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats
seq_composition0.0.51.70biopythonTo updateSequence compositionTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_compositionSequence Analysisseq_compositionpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition
seq_filter_by_id0.2.71.70biopythonTo updateFilter sequences by IDTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_idFasta Manipulation, Sequence Analysis, Text Manipulationseq_filter_by_idpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id
seq_filter_by_mapping0.0.71.70biopythonTo updateFilter sequencing reads using SAM/BAM mapping filesTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mappingAssembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysisseq_filter_by_mappingpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping
seq_length0.0.41.70biopythonTo updateCompute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)To updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_lengthFasta Manipulation, Fastq Manipulation, Sequence Analysisseq_lengthpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length
seq_primer_clip0.0.161.1.5galaxy_sequence_utilsTo updateTrim off 5' or 3' primersTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clipAssembly, Fasta Manipulation, Text Manipulationseq_primer_clippeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip
seq_rename0.0.91.1.5galaxy_sequence_utilsTo updateRename sequences with ID mapping from a tabular fileTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_renameFasta Manipulation, Sequence Analysis, Text Manipulationseq_renamepeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename
seq_select_by_id0.0.141.70biopythonTo updateSelect sequences by IDTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_idFasta Manipulation, Sequence Analysis, Text Manipulationseq_select_by_idpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id
venn_list0.1.11.1.5galaxy_sequence_utilsTo updateDraw Venn Diagram (PDF) from lists, FASTA files, etcTo updatehttps://github.com/peterjc/pico_galaxy/tree/master/tools/venn_listGraphics, Sequence Analysis, Visualizationvenn_listpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list
TrimNs0.1.01.0trimns_vgpTo updateTrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipelineTo updatehttps://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNsAssemblytrimnsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN
abricate1.0.11.0.1abricateUp-to-dateABRicateABRicateAntimicrobial resistance predictionGenomics, MicrobiologyMass screening of contigs for antiobiotic resistance genesMass screening of contigs for antimicrobial resistance or virulence genes.Up-to-datehttps://github.com/tseemann/abricateSequence Analysisabricateiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/
abritamr1.0.141.0.14abritamrUp-to-dateA pipeline for running AMRfinderPlus and collating results into functional classesUp-to-datehttps://zenodo.org/record/7370628Sequence Analysisabritamriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr
abyss2.3.62.3.7abyssTo updateabyssABySSGenome assembly, De-novo assemblySequence assemblyAssembly By Short Sequences - a de novo, parallel, paired-end sequence assemblerDe novo genome sequence assembler.To updatehttp://www.bcgsc.ca/platform/bioinfo/software/abyssAssemblyabyssiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss
adapter_removal2.3.32.3.3adapterremovalUp-to-dateadapterremovalAdapterRemovalSequence trimming, Sequence merging, Primer removalRemoves residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.Up-to-datehttps://github.com/MikkelSchubert/adapterremovalFasta Manipulation, Sequence Analysisadapter_removaliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/
add_input_name_as_column0.2.0pythonTo updateAdd input name as column on an existing tabular fileTo updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_columnText Manipulationadd_input_name_as_columnmvdbeekhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column
aegean0.16.00.16.0aegeanUp-to-dategaevalGAEVALSequence annotationSequence analysis, Gene structureAEGeAn toolkit wrappersGene Annotation EVAluation.Up-to-datehttps://github.com/BrendelGroup/AEGeAnTranscriptomics, Sequence Analysisaegeaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean
aldex21.26.01.32.0bioconductor-aldex2To updatealdex2ALDEx2Statistical inferenceGene expression, Statistics and probabilityPerforms analysis Of differential abundance taking sample variation into accountA differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.To updatehttps://github.com/ggloor/ALDEx_biocMetagenomicsaldex2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2
allegro@VER@.03allegroTo updateallegroAllegroSequence motif discoverySequence analysis, Transcription factors and regulatory sites, DNALinkage and haplotype analysis from deCODEIt does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.To updatehttp://www.decode.com/software/Variant Analysisallegroiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/
amplican1.14.01.22.1bioconductor-amplicanTo updateamplicanamplicanAlignment, Standardisation and normalisationPCR experiment, Statistics and probabilityAmpliCan is an analysis tool for genome editing.It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.To updatehttps://github.com/valenlab/amplicanSequence Analysisamplicaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican
ampvis22.7.22To updateampvisampvisAnalysis, VisualisationBiodiversityampvis2ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.To updatehttps://github.com/MadsAlbertsen/ampvis2/Metagenomicsampvis2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2
amrfinderplus3.11.263.11.26ncbi-amrfinderplusUp-to-dateamrfinderplusAMRFinderPlusAntimicrobial resistance predictionMicrobiology, Public health and epidemiology, Infectious disease"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms.AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organismsUp-to-datehttps://github.com/ncbi/amrSequence AnalysisAMRFinderPlusiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus
ancombc1.4.02.2.0bioconductor-ancombcTo updateancombcANCOMBCDifferential gene expression profilingMicrobial ecology, MetagenomicsPerforms analysis of compositions of microbiomes with bias correction.Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.To updatehttps://github.com/FrederickHuangLin/ANCOMBCMetagenomicsancombciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc
anndata0.7.50.6.22anndataTo updateImport, Export, Inspect and Manipulate Anndata and Loom objectsTo updatehttps://anndata.readthedocs.ioTranscriptomics, Sequence Analysisanndataiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/
annotatemyids3.17.03.17.0bioconductor-org.hs.eg.dbUp-to-dateannotatemyidsannotatemyidsAnnotationannotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packagesThis tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.Up-to-datehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyidsGenome annotationannotatemyidsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids
arriba2.4.02.4.0arribaUp-to-dateArriba detects fusion genes in RNA-Seq data after running RNA-STARUp-to-datehttps://github.com/suhrig/arribaSequence Analysis, Transcriptomicsarribaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba
art2014.11.03.02016.06.05artTo updateartARTConversionBioinformaticsSimulator for Illumina, 454, and SOLiD sequencing dataART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiDTo updateSequence Analysis, Data Sourceartiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/art
artic1.2.3articTo updatearticARTICSequence alignmentGenomicsThe artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus buildingA bioinformatics pipeline for working with virus sequencing data sequenced with nanoporeTo updatehttps://github.com/artic-network/fieldbioinformaticsSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/artic
assembly-stats17.0217.02rjchallis-assembly-statsUp-to-dateAssembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.Up-to-datehttps://github.com/rjchallis/assembly-statsAssemblyassembly_statsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats
augustus3.4.03.5.0augustusTo updateaugustusAUGUSTUSGene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, OperationGene transcripts, Gene and protein familiesAUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.To updatehttp://bioinf.uni-greifswald.de/augustus/Sequence Analysisaugustusbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus
b2btools3.0.5+galaxy03.0.6b2btoolsTo updateb2btoolsb2bToolsProtein disorder prediction, Protein secondary structure prediction, Protein feature detectionThis software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSATo updatehttps://bio2byte.beComputational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biologyiuc
bakta1.8.21.8.2baktaUp-to-dateBaktaBaktaGenome annotationGenomics, Data submission, annotation and curation, Sequence analysis"Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."Rapid & standardized annotation of bacterial genomes, MAGs & plasmidsUp-to-datehttps://github.com/oschwengers/baktaSequence Analysisbaktaiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta
bam_to_scidx1.0.1openjdkTo updateContains a tool that converts a BAM file to an ScIdx file.To updatehttps://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidxConvert Formatsbam_to_scidxiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx
bamutil1.0.15bamutilTo updatebamUtil is a repository that contains several programs that perform operations on SAM/BAM files.To updatehttps://github.com/statgen/bamUtilSequence Analysisbamutiliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil
bandage2022.092022.09bandage_ngUp-to-datebandageBandageSequence assembly visualisationGenomics, Sequence assemblyBandage - A Bioinformatics Application for Navigating De novo Assembly Graphs EasilyGUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.Up-to-datehttps://github.com/rrwick/BandageVisualizationbandageiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage
barcode_splitter0.18.4.00.18.6barcode_splitterTo updateA utility to split sequence files using multiple sets of barcodesTo updatehttps://bitbucket.org/princeton_genomics/barcode_splitter/Fastq Manipulationbarcode_splitteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter
baredsc1.1.21.1.2baredscUp-to-datebaredscbaredSCData retrieval, Expression correlation analysis, Differential gene expression profilingRNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probabilitybaredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.Up-to-datehttps://github.com/lldelisle/baredSCTranscriptomics, Visualizationbaredsciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc
barrnap1.2.20.9barrnapTo updatebarrnapBarrnapGene predictionGenomics, Model organisms, Model organismsContains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).To updateSequence Analysisbarrnapiuc
basil1.2.01.2.0anise_basilUp-to-dateBreakpoint detection, including large insertionsUp-to-datehttps://github.com/seqan/anise_basilVariant Analysisbasiliuc
bax2bam0.0.110.0.11bax2bamUp-to-dateBAX to BAM converterUp-to-datehttps://github.com/pacificbiosciences/bax2bam/Convert Formats, Sequence Analysisbax2bamiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam
bayescan2.12.0.1bayescanTo updatebayescanBayeScanStatistical inferenceGenetics, Evolutionary biology, Statistics and probability, DNA polymorphismDetecting natural selection from population-based genetic dataBAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.To updatehttp://cmpg.unibe.ch/software/BayeScan/index.htmlSequence Analysisbayescaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/
bbtools39.0139.01bbmapUp-to-dateBBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.Up-to-datehttps://jgi.doe.gov/data-and-tools/bbtools/Sequence Analysisbbtoolsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools
bcftools1.15.11.18bcftoolsTo updatebcftoolsBCFtoolsData handling, Variant callingGenetic variation, DNA polymorphism, GWAS study, Genotyping experimentBCFtools toolkit wrappersBCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.To updatehttps://samtools.github.io/bcftools/Variant Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools
bctools0.2.20.2.2bctoolsUp-to-datebctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0Up-to-datehttps://github.com/dmaticzka/bctoolsSequence Analysis, Transcriptomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
beacon22.0.02.0.0beacon2-ri-toolsUp-to-dateGA4GH Beaconbeacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).Up-to-datehttps://github.com/EGA-archive/beacon2-ri-tools/tree/mainVariant Analysisbeacon2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2
beagle5.2_21Apr21.3045.4_22Jul22.46ebeagleTo updateBeagle is a program for phasing and imputing missing genotypes.To updatehttps://faculty.washington.edu/browning/beagle/beagle.htmlVariant Analysisbeagleiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle
bedops2.4.412.4.41bedopsUp-to-dateBEDOPS: high-performance genomic feature operationsUp-to-datehttps://bedops.readthedocs.io/en/latest/Genomic Interval Operationsbedops_sortbediuchttps://bedops.readthedocs.io/
bedtools2.30.02.31.0bedtoolsTo updatebedtoolsBEDToolsMappingGenomicsbedtools is a powerful toolset for genome arithmeticBEDTools is an extensive suite of utilities for comparing genomic features in BED format.To updatehttps://github.com/arq5x/bedtools2Genomic Interval Operations, Text Manipulationbedtoolsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
bellerophon1.01.0bellerophonUp-to-dateFilter mapped reads where the mapping spans a junction, retaining the 5-prime read.Up-to-datehttps://github.com/davebx/bellerophonSequence Analysisbellerophoniuchttps://github.com/davebx/bellerophon
berokka0.2.30.2.3berokkaUp-to-dateBerokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.Up-to-datehttps://github.com/tseemann/berokkaFasta Manipulationberokkaiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka
binning_refiner1.4.31.4.3binning_refinerUp-to-datebinning_refinerBinning_refinerRead binning, Sequence clusteringMetagenomicsReconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.Improving genome bins through the combination of different binning programsUp-to-datehttps://github.com/songweizhi/Binning_refinerMetagenomicsbinning_refineriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/
bioext0.20.40.21.2python-bioextTo updateA suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more!To updatehttps://pypi.python.org/pypi/biopython-extensions/Next Gen Mappersiuchttps://github.com/davebx/bioext-gx/
bioinformatics_cafe0.1.0pythonTo updateMiscellanea of scripts for bioinformaticsTo updatehttps://github.com/dariober/bioinformatics-cafe/Sequence Analysisbioinformatics_cafembernthttps://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe
biom_format2.1.152.1.7biom-formatTo updateThe biom-format package provides a command line interface and Python API for working with BIOM files.To updatehttps://github.com/biocore/biom-formatMetagenomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format
bioperl1.11.7.8perl-bioperlTo updatebioperlBioPerlData handling, Service invocationGenomics, Software engineering, Data managementConverts GenBank format files to GFF3A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming.To updatehttps://bioperl.org/Sequence Analysisbp_genbank2gff3iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl
biscot2.3.32.3.3biscotUp-to-dateBionano scaffolding correction toolUp-to-datehttps://github.com/institut-de-genomique/biscotAssemblybiscotiuchttps://github.com/bgruening/iuc/tree/master/tools/biscot
blast1.7.01.7.0magicblastUp-to-dateMaps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptomeUp-to-datehttps://ncbi.github.io/magicblast/Next Gen Mappersmagicblastiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/blast
blastxml_to_gapped_gff31.10.6.6bcbiogffTo updateBlastXML to gapped GFF3To updateConvert Formats, Sequence Analysisblastxml_to_gapped_gff3iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3
bowtie22.5.02.5.2bowtie2To updatebowtie2Bowtie 2Read mappingMapping, Genomics, MappingBowtie2: Fast and sensitive read alignmentBowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.To updatehttp://bowtie-bio.sourceforge.net/bowtie2Next Gen Mappersbowtie2devteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2
bracken2.82.9brackenTo updatebrackenBrackenStatistical calculationMetagenomics, Microbial ecologyBayesian Reestimation of Abundance with KrakENStatistical method that computes the abundance of species in DNA sequences from a metagenomics sample.To updatehttps://ccb.jhu.edu/software/bracken/Sequence Analysis, Metagenomicsbrackeniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken
breseq0.35.50.38.1breseqTo updatebreseqbreseqPolymorphism detectionSequencing, Sequence analysis, DNA mutationPredicts mutations in microbial genomesRuns Breseq software on a set of fastq files.To updatehttps://github.com/barricklab/breseqVariant Analysisbreseqiuc
busco5.4.65.5.0buscoTo updatebuscoBUSCOSequence assembly validation, Scaffolding, Genome assembly, Transcriptome assemblySequence assembly, Genomics, Transcriptomics, Sequence analysisBUSCO assess genome and annotation completenessProvides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.To updatehttps://gitlab.com/ezlab/busco/-/releasesSequence Analysisbuscoiuc
bwa0.7.170.7.17bwaUp-to-datebwaBWAGenome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignmentMappingWrapper for bwa mem, aln, sampe, and samseFast, accurate, memory-efficient aligner for short and long sequencing readsUp-to-datehttp://bio-bwa.sourceforge.net/Next Gen Mappersbwadevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa
bwa_mem22.2.12.2.1bwa-mem2Up-to-datebwa-mem2Bwa-mem2Sequence alignmentMappingBwa-mem2 is the next version of the bwa-mem algorithm in bwa.Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.Up-to-datehttps://github.com/bwa-mem2/bwa-mem2Next Gen Mappersbwa_mem2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2
bwameth0.2.60.2.7bwamethTo updateFast and accurate alignment of BS-seq readsTo updatehttps://github.com/brentp/bwa-methSequence Analysis, Next Gen Mappersbwamethiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth
calculate_contrast_threshold1.0.0numpyTo updateCalculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.To updatehttps://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_thresholdVisualization, Genomic Interval Operations, SAMcalculate_contrast_thresholdiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold
calculate_numeric_param0.1.0To updateCalculate a numeric parameter value using integer and float values.To updateText Manipulationcalculate_numeric_paramiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param
cat5.2.35.2.3catUp-to-dateContig Annotation Tool (CAT)Up-to-datehttps://github.com/dutilh/CATMetagenomicscontig_annotation_tooliuchttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat
cdhit4.8.14.8.1cd-hitUp-to-datecd-hitcd-hitSequence clusteringSequencingCluster or compare biological sequence datasetsCluster a nucleotide dataset into representative sequences.Up-to-datehttp://weizhongli-lab.org/cd-hit/Sequence Analysis, Fasta Manipulationcd_hitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit
cemitool1.18.11.24.0bioconductor-cemitoolTo updatecemitoolCEMiToolEnrichment analysis, Pathway or network analysisGene expression, Transcriptomics, Microarray experimentGene co-expression network analysis toolIt unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.To updatehttps://www.bioconductor.org/packages/release/bioc/html/CEMiTool.htmlTranscriptomics, RNA, Statisticscemitooliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool
charts1.0.1r-getoptTo updateEnables advanced visualization options in Galaxy ChartsTo updateVisualizationchartsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/
checkm1.2.01.2.2checkm-genomeTo updatecheckmCheckMOperationGenomics, Phylogenomics, Phylogenetics, Taxonomy, MetagenomicsAssess the quality of microbial genomes recovered from isolates, single cells, and metagenomesCheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.To updatehttps://github.com/Ecogenomics/CheckMMetagenomicscheckmiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm
cherri0.70.8cherriTo updatecherricherriComputational Help Evaluating RNA-RNA interactionsCheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.To updatehttps://github.com/BackofenLab/CherriTranscriptomics, RNAiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri
chira1.4.31.4.3chiraUp-to-datechiraChiRARNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNAChimeric Read Annotator for RNA-RNA interactome dataChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.Up-to-datehttps://github.com/pavanvidem/chiraRNA, Transcriptomics, Sequence Analysischiraiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/chira
chopin21.0.7chopin2To updateDomain-Agnostic Supervised Learning with Hyperdimensional ComputingTo updatehttps://github.com/cumbof/chopin2Machine Learningchopin2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2
chromeister1.5.a1.5.achromeisterUp-to-dateultra-fast pairwise genome comparisonsUp-to-datehttps://github.com/estebanpw/chromeisterSequence Analysischromeisteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister
circexplorer22.3.82.3.8circexplorer2Up-to-datecircexplorer2CIRCexplorer2RNA splicing, Gene transcripts, Literature and languageComprehensive and integrative circular RNA analysis toolset.Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.Up-to-datehttps://github.com/YangLab/CIRCexplorer2RNA, Assemblycircexplorer2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2
circos0.69.80.69.9circosTo updategalactic_circosGalactic CircosSequence visualisationBuild Circos Plots in GalaxyGalactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format.To updatehttp://circos.ca/Graphicscircosiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/circos
cite_seq_count1.4.41.4.4cite-seq-countUp-to-dateCITE-seq-CountCITE-seq-CountRNA-Seq quantificationTranscriptomics, Immunoproteins and antigensCount CMO/HTOTool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.Up-to-datehttps://github.com/Hoohm/CITE-seq-CountTranscriptomicscite_seq_countiuchttps://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count
clair30.1.121.0.4clair3To updateclair3Clair3Variant callingMolecular geneticsSymphonizing pileup and full-alignment for high-performance long-read variant callingClair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.To updatehttps://github.com/HKU-BAL/Clair3Sequence Analysis, Variant Analysisclair3iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3
clustalw2.12.1clustalwUp-to-date\n clustalw\nClustalW multiple sequence alignment program for DNA or proteinsUp-to-datehttp://www.clustal.org/clustal2/Phylogenetics, Sequence Analysisclustalwdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw
cnvkit0.9.100.9.10cnvkitUp-to-datecnvkitCNVkitVariant callingDNA structural variationdetecting copy number variants and alterations genome-wide from high-throughput sequencingCNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.Up-to-datehttps://github.com/etal/cnvkitVariant Analysiscnvkitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit
codeml4.94.10.6pamlTo updateDetects positive selectionTo updatehttp://abacus.gene.ucl.ac.uk/software/paml.htmlPhylogeneticscodemliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml
cojac0.9.10.9.1cojacUp-to-datecojacCOJACGenetic variationco-occurrence of mutations on ampliconsCoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.Up-to-datehttps://github.com/cbg-ethz/cojacMetagenomics, Sequence Analysiscojaciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac
colibread24.7.14+galaxy024.7.14commetTo updateColib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genomeTo updatehttps://colibread.inria.fr/Sequence Analysis, Variant Analysiscolibreadiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread
collection_column_join0.0.38.25coreutilsTo updateColumn Join on CollectionsTo updateText Manipulationcollection_column_joiniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join
collection_element_identifiers0.0.2To updateExtract element identifiers of a collectionTo updateText Manipulationcollection_element_identifiersiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers
column_maker2.0pythonTo updateCompute an expression on every rowTo updateText Manipulationcolumn_makerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker
column_order_header_sort0.0.1pythonTo updateSort Column Order by headingTo updateText Manipulationcolumn_order_header_sortiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort
column_remove_by_header1.0pythonTo updateRemove columns by headerTo updateText Manipulationcolumn_remove_by_headeriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header
compose_text_param0.1.1To updateCompose a text parameter value using text, integer and float valuesTo updateText Manipulationcompose_text_paramiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param
compress_file0.1.0gzipTo updateCompress files.To updateText Manipulationcompress_fileiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file
concoct1.1.01.1.0concoctUp-to-dateCONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.Up-to-datehttps://github.com/BinPro/CONCOCTMetagenomicsconcoctiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct
coverage_report0.0.41.76perl-number-formatTo updateGenerate Detailed Coverage Report from BAM fileTo updatehttps://github.com/galaxyproject/tools-iucSequence Analysiscoverage_reportiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report
coverm0.6.10.6.1covermUp-to-datecovermCoverMLocal alignmentBioinformaticsCoverM genome and contig wrappersRead coverage calculator for metagenomicsUp-to-datehttps://github.com/wwood/CoverMSequence Analysiscovermiuchttps://github.com/galaxyproject/tools-iuc/tools/coverm
crispr_studio1+galaxy01crispr_studioTo updateCRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.To updatehttps://github.com/moineaulab/CRISPRStudioSequence Analysiscrispr_studioiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/
crosscontamination_barcode_filter0.32.2.1r-ggplot2To updateBarcode contamination discovery toolTo updateTranscriptomics, Visualizationcrosscontamination_barcode_filteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter
crossmap0.6.10.6.5crossmapTo updateCrossMap converts genome coordinates or annotation files between genome assembliesTo updatehttp://crossmap.sourceforge.net/Convert Formats, Genomic Interval Operationscrossmapiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap
cutadapt4.44.5cutadaptTo updatecutadaptCutadaptSequence trimmingGenomics, Probes and primers, SequencingFlexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.To updatehttps://cutadapt.readthedocs.org/en/stable/Fasta Manipulation, Fastq Manipulation, Sequence Analysiscutadaptlparsonshttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt
cutesv1.0.82.0.3cutesvTo updatecuteSVcuteSVSplit read mapping, Genotyping, Structural variation detectionDNA structural variation, Sequencing, Computer scienceLong-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysisTo updatehttps://github.com/tjiangHIT/cuteSVVariant Analysiscutesviuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv
cwpair21.1.1matplotlibTo updateContains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans.To updateChIP-seqcwpair2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2
dada21.28.0bioconductor-dada2To updatedada2dada2Variant calling, DNA barcodingSequencing, Genetic variation, Microbial ecology, MetagenomicsDADA2 wrappersThis package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.To updatehttps://benjjneb.github.io/dada2/index.htmlMetagenomicsdada2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2
das_tool1.1.61.1.6das_toolUp-to-datedastooldastoolRead binningMetagenomicsDAS Tool for genome resolved metagenomicsDAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.Up-to-datehttps://github.com/cmks/DAS_ToolMetagenomicsdas_tooliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool
data_source_iris_tcga1.0.0pythonTo updateIRIS-TCGA Data source toolTo updateData Sourcedata_source_iris_tcgaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga
datamash1.81.1.0datamashTo updateGNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon.To updatehttps://www.gnu.org/software/datamash/Text Manipulationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash
decontaminator1.0.0numpyTo updatedecontaminatorDeep Learning method for novel virus detection in sequencing dataTo updatehttps://github.com/cbib/decontaminatorMachine Learningdecontaminatoriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator
deepmicro1.41.4deepmicroUp-to-date\n DeepMicro\nRepresentation learning and classification frameworkUp-to-datehttps://github.com/paulzierep/DeepMicroMachine Learningdeepmicroiuchttps://github.com/paulzierep/DeepMicro
deepsig1.2.51.2.5deepsigUp-to-datePredictor of signal peptides in proteins based on deep learningUp-to-datehttps://github.com/BolognaBiocomp/deepsigGenome annotationdeepsigiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig
deepvariant1.5.0To updateDeepVariant is a deep learning-based variant callerTo updatehttps://github.com/google/deepvariantVariant Analysisdeepvariantiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant
deg_annotate1.1.02.31.0bedtoolsTo updateAnnotate DESeq2/DEXSeq output tablesTo updateTranscriptomicsdeg_annotateiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate
delly0.9.11.1.8dellyTo updatedelly2Delly2Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysisDNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseasesDelly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.To updatehttps://github.com/dellytools/dellyVariant Analysisdellyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/delly
deseq22.11.40.81.40.2bioconductor-deseq2To updateDESeq2DESeq2Differential gene expression analysisTranscriptomicsDifferential gene expression analysis based on the negative binomial distributionR/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.To updatehttps://www.bioconductor.org/packages/release/bioc/html/DESeq2.htmlTranscriptomics, RNA, Statisticsdeseq2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2
dexseq1.441.46.0bioconductor-dexseqTo updatedexseqDEXSeqEnrichment analysis, Exonic splicing enhancer predictionRNA-SeqInference of differential exon usage in RNA-SeqThe package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.To updatehttps://www.bioconductor.org/packages/release/bioc/html/DEXSeq.htmlTranscriptomics, RNA, Statisticsdexseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq
diamond2.0.152.1.8diamondTo updateDIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.To updatehttps://github.com/bbuchfink/diamondSequence Analysisdiamondbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond
diffbind2.10.0+galaxy03.10.0bioconductor-diffbindTo updatediffbindDiffBindDifferential binding analysisChIP-seqDiffbind provides functions for processing ChIP-Seq data.Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.To updatehttp://bioconductor.org/packages/release/bioc/html/DiffBind.htmlChIP-seqdiffbindbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind
dimet0.1.40.1.4dimetUp-to-dateDIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.Up-to-datehttps://github.com/cbib/DIMetMetabolomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet
disco1.2discoTo updatediscoDISCOProtein sequence analysisStructure determinationDISCO is a overlap-layout-consensus (OLC) metagenome assemblerDISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.To updatehttp://disco.omicsbio.org/Metagenomics, Assemblydiscoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/
dnabot3.1.0dnabotTo updateDNA assembly using BASIC on OpenTronsTo updatehttps://github.com/BASIC-DNA-ASSEMBLY/DNA-BOTSynthetic Biologydnabotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot
dnaweaver1.0.21.0.2dnaweaver_synbiocadUp-to-dateGiven a SBOL input, calculate assembly parts for Gibson or Golden Gate.Up-to-datehttps://github.com/Edinburgh-Genome-Foundry/DnaWeaverSynthetic Biologydnaweaveriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver
dram1.3.51.4.6dramTo updateDRAM for distilling microbial metabolism to automate the curation of microbiome functionTo updatehttps://github.com/WrightonLabCSU/DRAMMetagenomicsdramiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dram
drep3.4.33.4.5drepTo updatedrepdRepGenome comparisonMetagenomics, Genomics, Sequence analysisdRep compares and dereplicates genome setsFast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.To updatehttps://github.com/MrOlm/drepMetagenomicsdrepiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/drep
dropletutils1.10.01.20.0bioconductor-dropletutilsTo updatedropletutilsDropletUtilsLoading, Community profilingGene expression, RNA-seq, Sequencing, TranscriptomicsDropletUtils - Utilities for handling droplet-based single-cell RNA-seq dataProvides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.To updatehttps://bioconductor.org/packages/devel/bioc/html/DropletUtils.htmlTranscriptomics, Sequence Analysisdropletutilsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/
ebi_tools0.1.0sixTo updateTools to query and download data from several EMBL-EBI databasesTo updatehttp://www.ebi.ac.uk/services/allWeb Services, Data Sourceebi_toolsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools
edger3.36.03.42.4bioconductor-edgerTo updateedgeredgeRDifferential gene expression analysisGenetics, RNA-Seq, ChIP-seqPerform RNA-Seq differential expression analysis using edgeR pipelineDifferential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.To updatehttp://bioconductor.org/packages/release/bioc/html/edgeR.htmlTranscriptomics, RNA, Statisticsedgeriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/edger
egsea1.20.01.28.0bioconductor-egseaTo updateegseaEGSEAGene set testingSystems biologyThis tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testingThis package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.To updatehttps://bioconductor.org/packages/release/bioc/html/EGSEA.htmlTranscriptomics, RNA, Statisticsegseaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea
emboss_55.0.06.6.0embossTo updateembossEMBOSSSequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignmentMolecular biology, Sequence analysis, BiologyGalaxy wrappers for EMBOSS version 5.0.0 toolsDiverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.To updatehttp://emboss.open-bio.org/Sequence Analysis, Fasta Manipulationemboss_5devteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5
ena_upload0.6.30.6.3ena-upload-cliUp-to-dateSubmits experimental data and respective metadata to the European Nucleotide Archive (ENA).Up-to-datehttps://github.com/usegalaxy-eu/ena-upload-cliData Exportena_uploadiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload
enasearch0.2.2enasearchTo updateA Python library for interacting with ENA's APITo updatehttps://github.com/bebatut/enasearchData Sourceenasearchiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch
ensembl_vep110.1110.1ensembl-vepUp-to-dateEnsembl VEP: Annotate VCFs with variant effect predictionsUp-to-datehttps://github.com/Ensembl/ensembl-vepVariant Analysisensembl_vepiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep
episcanpy0.3.20.4.0episcanpyTo updateepiscanpyepiScanpyEnrichment analysis, ImputationEpigenomics, Cell biology, DNAEpiScanpy – Epigenomics single cell analysis in pythonEpigenomics Single Cell Analysis in Python.To updatehttps://github.com/colomemaria/epiScanpyEpigeneticsepiscanpyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/
exomedepth1.1.01.1.16r-exomedepthTo updateexomedepthExomeDepthSequence analysis, Variant calling, Genotyping, Copy number estimationExome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseasesExomeDepth: Calls copy number variants (CNVs) from targeted sequence dataCopy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.To updatehttps://cran.r-project.org/package=ExomeDepthSequence Analysis, Variant Analysisexomedepthcrs4https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth
exonerate2.4.02.4.0exonerateUp-to-dateexonerateExoneratePairwise sequence alignment, Protein threading, Genome alignmentSequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networksExonerate is a generic tool for pairwise sequence comparison.A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.Up-to-datehttps://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerateSequence Analysisexonerateiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate
export2graphlan0.200.22export2graphlanTo updateexport2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAnTo updatehttps://bitbucket.org/CibioCM/export2graphlan/overviewMetagenomicsexport2graphlaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/
extract_genomic_dna3.0.3+galaxy20.10.0bx-pythonTo updateContains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.To updateGenomic Interval Operationsextract_genomic_dnaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna
fargene0.10.1fargeneUp-to-datefARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )Up-to-datehttps://github.com/fannyhb/fargeneSequence Analysisfargeneiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene
fasta_nucleotide_color_plot1.0.1openjdkTo updateContains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.To updatehttps://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplotVisualizationfasta_nucleotide_color_plotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot
fasta_stats2.0numpyTo updateDisplay summary statistics for a fasta file.To updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/Sequence Analysisfasta_statsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/
fastani1.31.34fastaniTo updateFast alignment-free computation of whole-genome Average Nucleotide IdentityTo updatehttps://github.com/ParBLiSS/FastANISequence Analysisfastaniiuc
fastp0.23.4fastpTo updateFast all-in-one preprocessing for FASTQ filesTo updatehttps://github.com/OpenGene/fastpSequence Analysisfastpiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp
fastqc0.74+galaxy00.12.1fastqcTo updatefastqcFastQCSequence composition calculation, Sequencing quality control, Statistical calculationSequencing, Data quality management, Sequence analysisRead QC reports using FastQCThis tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.To updatehttp://www.bioinformatics.babraham.ac.uk/projects/fastqc/Fastq Manipulationfastqcdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc
fastqe0.2.6+galaxy20.3.1fastqeTo updateFASTQETo updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqeSequence Analysisfastqeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe
fasttree2.1.102.1.11fasttreeTo updatefasttreeFastTreePhylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)Phylogenetics, Sequence analysisFastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVLInfers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.To updatehttp://www.microbesonline.org/fasttree/Phylogeneticsfasttreeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree
featurecounts2.0.32.0.6subreadTo updatefeaturecountsFeatureCountsRead summarisationSequencingfeatureCounts counts the number of reads aligned to defined masked regions in a reference genomefeatureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.To updatehttp://bioinf.wehi.edu.au/featureCountsRNA, Transcriptomics, Sequence Analysisfeaturecountsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts
feelnc0.2.10.2feelncTo updatefeelncFEELncAnnotation, ClassificationRNA-seq, Functional, regulatory and non-coding RNAGalaxy wrapper for FEELncA tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.To updatehttps://github.com/tderrien/FEELncSequence Analysisfeelnciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc
fermikitr193r193fermi2Up-to-dateFermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.Up-to-datehttps://github.com/lh3/fermikitAssembly, Variant Analysisfermikitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit
fgsea1.8.0+galaxy11.26.0bioconductor-fgseaTo updatefgseafgseaGene-set enrichment analysisGeneticsPerform gene set testing using fgseaThe package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.To updatehttps://bioconductor.org/packages/release/bioc/html/fgsea.htmlVisualization, Transcriptomics, Statisticsfgseaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea
filtlong0.2.10.2.1filtlongUp-to-date\n filtlong\nFiltlong - Filtering long reads by qualityUp-to-datehttps://github.com/rrwick/FiltlongFastq Manipulation, Sequence Analysisfiltlongiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong
flair1.52.0.0flairTo updateFLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.To updatehttps://github.com/BrooksLabUCSC/flairNanoporeflairiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/flair
flash1.2.111.2.11flashUp-to-dateflashFLASHRead pre-processing, Sequence merging, Sequence assemblySequencing, Sequence assemblyFast Length Adjustment of SHort readsIdentifies paired-end reads which overlap in the middle, converting them to single long readsUp-to-datehttps://ccb.jhu.edu/software/FLASH/Assembly, Fastq Manipulationflashiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/flash
fraggenescan1.31fraggenescanTo updatefraggenescanFragGeneScanGene predictionGenetics, Sequence analysisTool for finding (fragmented) genes in short readApplication for finding (fragmented) genes in short readsTo updatehttps://sourceforge.net/projects/fraggenescan/Sequence Analysisfraggenescaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/
freebayes1.3.61.3.7freebayesTo updatefreebayesFreeBayesVariant calling, Statistical calculationGenomics, Genetic variation, Rare diseasesGalaxy Freebayes Bayesian genetic variant detector toolBayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.To updatehttps://github.com/ekg/freebayesVariant Analysisfreebayesdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes
freec11.6gawkTo updatefreecFREECCopy number estimation, Variant calling, Genome alignmentDNA structural variation, Oncology, Human genetics, Data miningControl-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.To updatehttp://boevalab.inf.ethz.ch/FREEC/Variant Analysiscontrol_freeciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/freec
freyja1.4.41.4.7freyjaTo updatefreyjalineage abundances estimationTo updatehttps://github.com/andersen-lab/FreyjaMetagenomics, Sequence Analysisfreyjaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja
fsd1.0.2matplotlibTo updateTool that plots a histogram of sizes of read familiesTo updateGraphicsduplex_family_size_distributioniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd
funannotate1.8.15To update\n funannotate\nFunannotate is a genome prediction, annotation, and comparison software package.To updatehttps://funannotate.readthedocs.ioGenome annotationiuchttps://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate
gatk44.1.7.04.4.0.0gatk4To updateA Galaxy wrapper for Mutect2 from GATKTo updatehttps://software.broadinstitute.org/gatk/gatk4Variant Analysisgatk4_mutect2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4
gdcwebapp1.0.0pythonTo updateGDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED formatTo updatehttp://bioinf.iasi.cnr.it/gdcwebapp/Data Source, Convert Formatsgdcwebappiuchttps://github.com/fabio-cumbo/GDCWebApp4Galaxy
gecko1.21.2geckoUp-to-dateUngapped genome comparisonUp-to-datehttps://github.com/otorreno/geckoSequence Analysisgeckoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko
gemini0.20.10.30.2geminiTo updategeminiGEMINISequence analysis, Genetic variation analysisSequence analysisGEMINI: a flexible framework for exploring genome variationGEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.To updatehttps://github.com/arq5x/geminiSequence Analysis, Next Gen Mappersgeminiiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini
genebed_maf_to_fasta1.0.1+galaxy0To updateStitch gene blocks given a set of coding exon intervalsTo updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/Genomic Interval Operationsgenebed_maf_to_fastaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/
genehunter_modscore3.0.03.1ghmTo updateMaximised LOD score pedigree analysis utilityTo updatehttps://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-modscore/index.htmlVariant Analysisgenehunter_modscoreiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/
geneiobio4.7.1+galaxy1To updateGene.iobio is an interactive tool for variant and trio analysis.To updatehttps://github.com/iobio/gene.iobioSequence Analysisgeneiobioiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio
genetracknumpyTo updateContains a tool that separately identifies peaks on the forward "+” (W) and reverse “-” (C) strand.To updateChIP-seqgenetrackiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack
genomescope2.02.0genomescope2Up-to-dateAnalyze unassembled short readsUp-to-datehttps://github.com/tbenavi1/genomescope2.0Statisticsgenomescopeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope
genomic_super_signature1.2.01.8.0bioconductor-genomicsupersignatureTo updategenomicsupersignatureGenomicSuperSignatureGene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reductionRNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experimentInterpretation of RNAseq experiments through robust, efficient comparison to public databasesGenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.To updatehttps://github.com/shbrief/GenomicSuperSignatureSequence Analysis, RNA, Transcriptomicsgenomic_super_signatureiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature
genrich0.5+galaxy20.6.1genrichTo updateGenrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).To updatehttps://github.com/jsh58/GenrichChIP-seqgenrichiuchttps://github.com/jsh58/Genrich
get_hrun0.5.9.20.7.2.1pyfaidxTo updateAnnotate indel variants with homopolymer contextTo updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrunVariant Analysisget_hruniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun
getorganelle1.7.7.01.7.7.0getorganelleUp-to-dategetorganelleGetOrganelleDe-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimmingCell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organismsGetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.Up-to-datehttps://github.com/Kinggerm/GetOrganelleAssemblygetorganelleiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle
gfa_to_fa0.1.2To updategfa_to_fa - Converting GFA format to Fasta formatTo updatehttp://gfa-spec.github.io/GFA-spec/Convert Formatsgfa_to_faiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa
gff3_rebase1.20.6.6bcbiogffTo updateRebase a GFF against a parent GFF (e.g. an original genome)To updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebaseSequence Analysisgff3_rebaseiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase
gffcompare0.12.60.12.6gffcompareUp-to-dategffcomparegffcompareSequence annotationNucleic acids, Sequence analysisGalaxy wrappers for Geo Pertea's GffCompare package.Program for comparing, annotating, merging and tracking transcripts in GFF files.Up-to-datehttps://github.com/gpertea/gffcompare/Transcriptomicsgffcompareiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare
gffread0.12.70.12.7gffreadUp-to-dategffreadgffreadSequence annotationNucleic acids, Sequence analysisgffread filters and/or converts GFF3/GTF2 recordsprogram for filtering, converting and manipulating GFF filesUp-to-datehttp://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/Sequence Analysisgffreaddevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread
ggplot23.4.0r-baseTo updateggplot2ggplot2VisualisationData visualisationggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.Plotting system for R, based on the grammar of graphics.To updatehttps://github.com/tidyverse/ggplot2Visualizationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2
ggupset1.0r-ggupsetTo updateCreate Upset Plots with ggupsetTo updatehttps://github.com/const-ae/ggupsetGraphicsggupsetiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset
glimmer3.02glimmerTo updategeminiGEMINISequence analysis, Genetic variation analysisSequence analysisGlimmer makes gene predictions.GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.To updatehttps://ccb.jhu.edu/software/glimmer/Sequence Analysisbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer
goenrichment2.0.12.0.1goenrichmentUp-to-dategoenrichmentGOEnrichmentGene-set enrichment analysisTranscriptomicsPerforms GO Enrichment analysis.GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de CiĂŞncia.Up-to-datehttps://github.com/DanFaria/GOEnrichmentGenome annotationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment
goseq1.50.01.52.0bioconductor-goseqTo updategoseqGOseqGene functional annotationRNA-seqgoseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq dataDetect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.To updatehttps://bioconductor.org/packages/release/bioc/html/goseq.htmlStatistics, RNA, Micro-array Analysisgoseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq
gprofiler@TOOL_VERSION@+galaxy11r-gprofiler2To updatefunctional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and moreTo updatehttps://biit.cs.ut.ee/gprofilerStatistics, Web Servicesgprofileriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/
graphembed2.42.4graph_embedUp-to-dateCompute a 2D embedding of a data matrix given supervised class informationUp-to-datehttps://github.com/fabriziocosta/GraphEmbedStatistics, Graphicsgraphembediuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/
graphlan1.1.3graphlanTo updateGraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic treesTo updatehttps://bitbucket.org/nsegata/graphlan/overviewMetagenomics, Graphics, Phylogeneticsgraphlaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/
gtdbtk2.2.22.3.2gtdbtkTo updateGTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes.To updatehttps://github.com/Ecogenomics/GTDBTkMetagenomicsgtdbtkiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk
gtfToBed12357447ucsc-gtftogenepredTo updateUCSC_Genome_Browser_UtilitiesUCSC Genome Browser UtilitiesSequence analysisConvert GTF files to BED12 formatUtilities for handling sequences and assemblies from the UCSC Genome Browser project.To updatehttp://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/READMEConvert Formatsgtftobed12iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12
gubbins3.2.13.3.1gubbinsTo updategubbinsGubbinsGenotyping, Phylogenetic inference, Ancestral reconstructionPhylogeny, Genotype and phenotype, Whole genome sequencingGubbins - bacterial recombination detectionGubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.To updateSequence Analysisgubbinsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins
gvcftools0.10.17.0gvcftoolsTo updateTo updatehttps://github.com/sequencing/gvcftoolsVariant Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools
gwastools0.1.01.46.0bioconductor-gwastoolsTo updategwastoolsGWASToolsDeposition, Analysis, AnnotationGWAS studyClasses for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.To updatehttps://bioconductor.org/packages/release/bioc/html/GWASTools.htmlVisualization, Variant Analysisiuc
hamronization1.0.31.1.4hamronizationTo updateConvert AMR gene detection tool output to hAMRonization specification format.To updatehttps://github.com/pha4ge/hAMRonizationSequence Analysishamronizationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization
hansel2.6.12.6.1bio_hanselUp-to-dateHeidelberg and Enteritidis SNP ElucidationUp-to-datehttps://github.com/phac-nml/bio_hanselSequence Analysisbio_hanseliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel
hapcut21.3.31.3.3hapcut2Up-to-datehapcut2HapCUT2Haplotype mapping, Variant classificationRobust and accurate haplotype assembly for diverse sequencing technologiesHapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.mdUp-to-datehttps://github.com/vibansal/HapCUT2Assemblyhapcut2galaxy-australiahttps://github.com/galaxyproject/tools-iuc
hapog1.3.61.3.6hapogUp-to-dateHapo-G - Haplotype-Aware Polishing of GenomesUp-to-datehttps://github.com/institut-de-genomique/HAPO-GAssemblyhapogiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog
happy0.3.140.3.15hap.pyTo updatehap.pyhap.pyVariant calling, Sequence analysis, GenotypingGenomics, DNA polymorphismA tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison.To updatehttps://github.com/Illumina/hap.pyVariant Analysishappyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/happy
heatmap23.1.32.17.0r-gplotsTo updateheatmap.2 function from the R gplots packageTo updatehttps://github.com/cran/gplotsVisualizationggplot2_heatmap2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2
heinz1.01.60.0bioconductor-bionetTo updatebionetBioNetProtein interaction analysisMolecular interactions, pathways and networks, Protein interactionsAn algorithm for identification of the optimal scoring subnetwork.This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from these p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.To updatehttps://github.com/ls-cwi/heinzTranscriptomics, Visualization, Statisticsheinziuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz
hicexplorer3.7.23.7.2hicexplorerUp-to-dateHiCExplorer: Set of programs to process, analyze and visualize Hi-C data.Up-to-datehttps://github.com/deeptools/HiCExplorerSequence Analysis, Visualizationhicexplorerbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer
hicstuff3.1.53.2.1hicstuffTo updateTo updatehttps://github.com/koszullab/hicstuffSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff
hifiasm_meta0.3.1hamtv0.3.1hifiasm_metaTo updateA hifiasm fork for metagenome assembly using Hifi reads.To updatehttps://github.com/xfengnefx/hifiasm-metaMetagenomicshifiasm_metagalaxy-australiahttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta
hisat22.2.12.2.1hisat2Up-to-datehisat2HISAT2Sequence alignmentRNA-seqHISAT2 is a fast and sensitive spliced alignment program.Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).Up-to-datehttp://ccb.jhu.edu/software/hisat2/Assemblyhisat2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2
hivclustering1.3.11.6.8python-hivclusteringTo updateInfers transmission networks from pairwise distances inferred by tn93To updatehttps://pypi.org/project/hivclustering/Next Gen Mappershivclusteringiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/
hmmer33.3.23.3.2hmmerUp-to-datehmmer3HMMER3Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database searchSequence analysis, Sequence sites, features and motifs, Gene and protein familiesHMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.Up-to-datehttp://hmmer.org/Sequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3
homer4.114.11homerUp-to-datehomerhomerSequence motif discoveryHOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.Up-to-datehttp://homer.ucsd.edu/homer/index.htmlSequence Analysisdata_manager_homer_preparseiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/homer
htseq_count0.9.1+galaxy12.0.3htseqTo updatehtseqHTSeqNucleic acid sequence analysisSequence analysisCount aligned reads (SAM/BAM) that overlap genomic features (GFF)Python framework to process and analyse high-throughput sequencing (HTS) dataTo updatehttps://readthedocs.org/projects/htseq/Genomic Interval Operations, SAM, Sequence Analysis, RNAhtseq_countlparsonshttps://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count
humann3.83.8humannUp-to-datehumannhumannSpecies frequency estimation, Taxonomic classification, Phylogenetic analysisMetagenomics, PhylogenomicsHUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolutionHUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”Up-to-datehttp://huttenhower.sph.harvard.edu/humannMetagenomicshumanniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/humann
hybpiper2.1.62.1.6hybpiperUp-to-dateHybPiperHybPiperSequence trimming, Sequence assembly, Read mappingPhylogenetics, Plant biology, Gene transcripts, Sequence assembly, PhylogenomicsAnalyse targeted sequence capture dataParalogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.Up-to-datehttps://github.com/mossmatters/HybPiperSequence Analysis, Phylogeneticshybpiperiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper
hyphy2.5.472.5.50hyphyTo updateHyPhyHyPhyStatistical calculationPhylogeny, Small molecules, Molecular interactions, pathways and networksHypothesis Testing using PhylogeniesSoftware package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.To updatehttp://www.hyphy.orgPhylogeneticsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/
hypo1.0.31.0.3hypoUp-to-dateHyPoHyPoOptimisation and refinement, Genome assemblySequence assembly, GenomicsSuper Fast & Accurate Polisher for Long Read Genome AssembliesHyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.Up-to-datehttps://github.com/kensung-lab/hypoAssemblyhypoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo
icescreen1.2.01.2.0icescreenUp-to-dateICEscreenICEscreenDatabase search, Protein feature detectionMobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variationICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Firmicutes genomes.A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.Up-to-datehttps://icescreen.migale.inrae.fr/Genome annotationicescreeniuchttps://forgemia.inra.fr/ices_imes_analysis/icescreen
idba_ud1.1.3idbaTo updateidbaIDBASequence assemblySequence assemblyWrappers for the idba assembler variants.A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.To updatehttps://i.cs.hku.hk/~alse/hkubrg/projects/index.htmlAssemblyidbaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud
idr2.0.32.0.4.2idrTo updateGalaxy wrappers for the IDR package from Nathan BoleuTo updatehttps://github.com/nboley/idrSequence Analysisidriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/
idr_download0.445.11.1omero-pyTo updateImage Data Resource downloading toolTo updatehttps://idr.openmicroscopy.orgData Sourceidr_download_by_idsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download
iedb_api2.15.2pythonTo updateGet epitope binding predictions from IEDB-APITo updatehttp://tools.immuneepitope.org/main/tools-api/Data Source, Sequence Analysisiedb_apiiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api
instrain1.5.31.8.0instrainTo updateInStrain is a tool for analysis of co-occurring genome populations from metagenomesTo updatehttps://instrain.readthedocs.io/en/latest/#Metagenomicsinstrainiuchttps://github.com/MrOlm/inStrain
integron_finder2.0.23.3.2hmmerTo updateintegron_finderIntegron FinderNucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotationFunctional genomics, Mobile genetic elements, Molecular biology, Sequence analysis"IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"A tool to detect Integron in DNA sequences.To updatehttps://github.com/gem-pasteur/Integron_FinderSequence Analysisintegronfinderiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder
intermine_galaxy_exchange0.0.18.25coreutilsTo updateInterMine ExporterTo updateConvert Formatsintermine_galaxy_exchangeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange
interproscan5.59-91.05.59_91.0interproscanTo updateinterproscan_ebiInterProScan (EBI)Sequence motif recognition, Protein feature detectionGene and protein families, Sequence analysisInterproscan queries the interpro database and provides annotations.Scan sequences against the InterPro protein signature databases.To updatehttp://www.ebi.ac.uk/Tools/pfa/iprscan5/Sequence Analysisinterproscanbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan
interval2maf1.0.1+galaxy10.10.0bx-pythonTo updatebx-pythonbx-pythonSequence analysisExtract MAF blocks given a set of intervalsTools for manipulating biological data, particularly multiple sequence alignments.To updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/Genomic Interval Operationsinterval2mafiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/
intervene0.6.50.6.5interveneUp-to-dateinterveneInterveneSequence comparison, Sequence visualisationComputational biologyCreate pairwise and upset plotsTool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.Up-to-datehttps://intervene.readthedocs.ioStatisticsinterveneiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene
iqtree2.1.22.2.5iqtreeTo updateEfficient phylogenomic software by maximum likelihoodTo updatehttp://www.iqtree.org/Phylogeneticsiqtreeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/
irissv1.0.41.18samtoolsTo updateRefine insertion sequencesTo updatehttps://github.com/mkirsche/IrisVariant Analysisirissviuchttps://github.com/galaxyproject/tools-iuc/tools/irissv/
isescan1.7.2.31.7.2isescanTo updateISEScanISEScanStructural variation detectionGenomics, DNA structural variation, Sequence analysis, Genetic variation"ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."Automated identification of insertion sequence elements in prokaryotic genomes.To updatehttps://github.com/xiezhq/ISEScanSequence AnalysisISEScaniuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan
isoformswitchanalyzer1.20.02.0.1bioconductor-isoformswitchanalyzerTo updateIsoformSwitchAnalyzeRIsoformSwitchAnalyzeRSequence comparison, Sequence analysisComputational biology, Gene transcriptsStatistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.To updatehttps://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.htmlTranscriptomics, RNA, Statisticsisoformswitchanalyzeriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer
ivar1.4.21.4.2ivarUp-to-dateiVar is a computational package that contains functions broadly useful for viral amplicon-based sequencingUp-to-datehttps://github.com/andersen-lab/ivarSequence Analysisivariuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/
iwtomics1.0.01.24.0bioconductor-iwtomicsTo updateiwtomicsIWTomicsDifferential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, ComparisonStatistics and probabilityInterval-Wise Testing for Omics DataImplementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.To updatehttps://bioconductor.org/packages/release/bioc/html/IWTomics.htmlStatisticsiwtomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics
jasminesv1.0.111.1.5jasminesvTo updateMerge structural variants across samplesTo updatehttps://github.com/mkirsche/Jasmine/Variant Analysisjasminesviuchttps://github.com/galaxyproject/tools-iuc/jasminesv/
jbrowse1.16.111.16.11jbrowseUp-to-datejbrowseJBrowseGenome visualisationGenomicsJBrowse Genome Browser integrated as a Galaxy ToolSlick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.Up-to-datehttps://jbrowse.orgSequence Analysisjbrowseiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse
jcvi_gff_stats0.8.41.3.8jcviTo updateCompute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)To updatehttps://github.com/tanghaibao/jcviSequence Analysisjcvi_gff_statsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats
jellyfish2.3.0kmer-jellyfishTo updateJellyfishJellyfishk-mer countingSequence analysis, GenomicsJellyfish is a tool for fast, memory-efficient counting of k-mers in DNAA command-line algorithm for counting k-mers in DNA sequence.To updatehttps://github.com/gmarcais/JellyfishAssemblyjellyfishiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish
join_files_by_id1.01.11.6r-data.tableTo updateThis tool will join datasets according to a column with identifierTo updateText Manipulationjoin_files_by_idiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id
jq1.01.5jqTo updateJQ is a lightweight and flexible command-line JSON processorTo updatehttps://stedolan.github.io/jq/Text Manipulationjqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/jq
jvarkit2020122320201223jvarkit-wgscoverageplotterUp-to-dateJvarkit : Java utilities for BioinformaticsUp-to-datehttps://lindenb.github.io/jvarkit/SAMjvarkitiuchttps://github.com/galaxyproject/iuc/tree/master/tools/jvarkit
kallisto0.48.00.50.0kallistoTo updatekallistokallistoGene expression profilingTranscriptomics, RNA-seq, Gene expressionkallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.To updatehttps://pachterlab.github.io/kallisto/Transcriptomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/
kc-align1.0.21.0.2kcalignUp-to-datekc-alignkc-alignMultiple sequence alignmentMappingKc-Align custom toolA fast and accurate tool for performing codon-aware multiple sequence alignmentsUp-to-datehttps://github.com/davebx/kc-alignSequence Analysiskc_aligniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align
khmer3.0.0a33.0.0a3khmerUp-to-datekhmerkhmerStandardisation and normalisation, De-novo assemblySequence assemblyIn-memory nucleotide sequence k-mer counting, filtering, graph traversal and morekhmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.Up-to-datehttps://khmer.readthedocs.org/Assembly, Next Gen Mapperskhmeriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer
king2.2.72.2.7kingUp-to-dateKinship-based INference for GwasUp-to-datehttp://people.virginia.edu/~wc9c/KING/Variant Analysiskingiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/king/
kleborate2.3.22.3.2kleborateUp-to-datekleborateKleborateMultilocus sequence typing, Genome assembly, Virulence predictionPublic health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencingScreen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).Up-to-datehttps://github.com/katholt/Kleborate/wikiMetagenomicskleborateiuchttps://github.com/katholt/Kleborate
kma1.2.211.4.9kmaTo updateMap with KMATo updatehttps://bitbucket.org/genomicepidemiology/kmaNext Gen Mapperskmaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kma
kofamscan1.3.01.3.0kofamscanUp-to-dateGene function annotation tool based on KEGG Orthology and hidden Markov modelUp-to-datehttps://github.com/takaram/kofam_scanSequence Analysiskofamscaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan
kraken_biom1.2.01.2.0kraken-biomUp-to-dateCreate BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)Up-to-datehttps://github.com/smdabdoub/kraken-biomMetagenomicskraken_biomiuchttps://github.com/smdabdoub/kraken-biom
kraken_taxonomy_report0.0.31.70biopythonTo updateKraken taxonomy reportTo updatehttps://github.com/blankenberg/Kraken-Taxonomy-ReportMetagenomicskraken_taxonomy_reportiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report
krakentools1.21.2krakentoolsUp-to-datekrakentoolsKrakenToolsVisualisation, AggregationTaxonomy, MetagenomicsKrakenTools is a suite of scripts to be used alongside the KrakenKrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output filesUp-to-datehttps://github.com/jenniferlu717/KrakenToolsMetagenomicskrakentoolsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools
krocus1.0.11.0.3krocusTo updatePredict MLST directly from uncorrected long readsTo updatehttps://github.com/quadram-institute-bioscience/krocusSequence Analysiskrocusiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus
last12051454lastTo updatelastLASTSequence alignmentGenomics, Comparative genomicsLAST finds similar regions between sequences.Short read alignment program incorporating quality scoresTo updatehttp://last.cbrc.jp/Sequence Analysislastiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/last
lastz1.04.221.04.22lastzUp-to-datelastzLASTZSequence alignment, Read mappingGenomicsGalaxy wrappers for the Lastz and Lastz_dA tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.Up-to-datehttps://github.com/lastz/lastzNext Gen Mapperslastzdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz
lcrgenie1.0.2lcr_genieTo updateLigase Chain Reaction GenieTo updatehttps://github.com/neilswainston/LCRGenieSynthetic Biologylcrgenieiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie
legsta0.5.10.5.1legstaUp-to-datePerforms in silico Legionella pneumophila sequence based typing.Up-to-datehttps://github.com/tseemann/legstaSequence Analysislegstaiuchttps://github.com/tseemann/legsta
length_and_gc_content0.1.21.3.2r-optparseTo updateGets gene length and gc content from a fasta and a GTF fileTo updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_contentFasta Manipulation, Statistics, RNA, Micro-array Analysislength_and_gc_contentiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content
limma_voom3.50.13.56.2bioconductor-limmaTo updatelimmalimmaRNA-Seq analysisMolecular biology, GeneticsPerform RNA-Seq differential expression analysis using limma voom pipelineData analysis, linear models and differential expression for microarray data.To updatehttp://bioconductor.org/packages/release/bioc/html/limma.htmlTranscriptomics, RNA, Statisticslimma_voomiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom
lineagespot1.4.0r-baseTo updatelineagespotlineagespotVariant callingMetagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variationIdentification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).To updatehttps://www.bioconductor.org/packages/release/bioc/html/lineagespot.htmlMetagenomics, Sequence Analysislineagespotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot
links2.0.12.0.1linksUp-to-datelinksLINKSScaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimmingSequence assembly, Mapping, SequencingScaffold genome assemblies with long reads.LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.Up-to-datehttps://github.com/bcgsc/LINKSAssemblylinksiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/links
lofreq2.1.52.1.5lofreqUp-to-dateLoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.Up-to-datehttps://csb5.github.io/lofreq/Variant Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq
lorikeet2020lorikeetUp-to-dateTools for M. tuberculosis DNA fingerprinting (spoligotyping)Up-to-datehttps://github.com/AbeelLab/lorikeetSequence Analysislorikeet_spoligotypeiuchttps://github.com/AbeelLab/lorikeet
lumpy_sv0.3.10.3.1lumpy-svUp-to-dateLUMPY - a general probabilistic framework for structural variant discoveryUp-to-datehttp://layerlab.org/software/Variant Analysislumpy_sviuchttps://github.com/arq5x/lumpy-sv
m6anet2.1.02.1.0m6anetUp-to-datem6Anetm6AnetQuantification, Imputation, Gene expression profilingRNA-Seq, Transcriptomics, RNA, Machine learningm6anet to detect m6A RNA modifications from nanopore dataDetection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.Up-to-datehttps://m6anet.readthedocs.io/en/latestSequence Analysism6anetiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet
maaslin20.99.120.99.12maaslin2Up-to-dateMaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.Up-to-datehttp://huttenhower.sph.harvard.edu/maaslinMetagenomicsmaaslin2iuchttps://github.com/biobakery/Maaslin2
macs22.2.9.12.2.9.1macs2Up-to-datemacsMACSPeak calling, Enrichment analysis, Gene regulatory network analysisChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sitesMACS - Model-based Analysis of ChIP-SeqModel-based Analysis of ChIP-seq data.Up-to-datehttps://github.com/taoliu/MACSSequence Analysis, Statisticsmacs2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2
maf_stats1.0.2+galaxy0To updateMAF Coverage statisticsTo updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/Genomic Interval Operationsmaf_statsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/
mageck0.5.9.20.5.9mageckTo updatemageckMAGeCKGenetic variation analysisGenetics, Genetic variation, GenomicsModel-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.To updatehttps://sourceforge.net/projects/mageck/Genome editingiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck
maker2.31.113.01.03makerTo updatemakerMAKERGenome annotationGenomics, DNA, Sequence analysisMAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.To updatehttp://www.yandell-lab.org/software/maker.htmlSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/maker
malt0.5.30.61maltTo updateAligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences.To updatehttps://github.com/husonlab/maltNext Gen Mappersmalt_runiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/malt
map_param_value0.1.1To updateMap a parameter value to another valueTo updateText Manipulationmap_param_valueiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value
mapseq2.1.1perlTo updatefast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.To updatehttps://github.com/jfmrod/MAPseqMetagenomicsmapseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq
mash2.32.3mashUp-to-datemashMashSequence distance matrix generationGenomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutationFast genome and metagenome distance estimation using MinHashFast genome and metagenome distance estimation using MinHash.Up-to-datehttps://github.com/marbl/MashMetagenomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mash
masigpro1.49.38.25coreutilsTo updatemasigpromaSigProRegression analysisGene expression, Molecular genetics, Microarray experiment, RNA-SeqIdentify significantly differential expression profiles in time-course microarray experimentsRegression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.To updatehttps://www.bioconductor.org/packages/release/bioc/html/maSigPro.htmlTranscriptomics, RNA, Statisticsmasigproiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro
maxbin22.2.7maxbin2To updatemaxbinMaxBinSequence assemblyMetagenomics, Sequence assembly, Microbiologyclusters metagenomic contigs into binsSoftware for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.To updatehttps://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.htmlMetagenomicsmaxbin2mbernthttps://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/
mcl14.13722.282mclTo updatemclMCLClustering, Network analysis, Gene regulatory network analysisMolecular interactions, pathways and networksThe Markov Cluster Algorithm, a cluster algorithm for graphsMCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.To updatehttps://micans.org/mcl/man/mcl.htmlmcliuchttps://github.com/galaxyproject/tools-iuc/tree/master/mcl
medaka1.7.21.11.1medakaTo updatemedakaMedakaBase-calling, Variant calling, Sequence assemblySequence assembly, Machine learningSequence correction provided by ONT Researchmedaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.To updatehttps://github.com/nanoporetech/medakaSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka
megahit1.2.91.2.9megahitUp-to-datemegahitMEGAHITGenome assemblyMetagenomics, Sequencing, Ecology, Sequence assemblyAn ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.Up-to-datehttps://github.com/voutcn/megahitSequence Analysis, Assembly, Metagenomicsmegahitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit
megahit_contig2fastg1.1.31.2.9megahitTo updatemegahitMEGAHITGenome assemblyMetagenomics, Sequencing, Ecology, Sequence assemblyA subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.To updatehttps://github.com/voutcn/megahit/blob/master/tools/toolkit.cppSequence Analysis, Assembly, Metagenomicsmegahit_contig2fastgiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg
megan6.21.76.24.20meganTo updatemeganMEGANSequence analysis, Taxonomic classificationSequence analysisMEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzerÂť) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.To updatehttps://github.com/husonlab/megan-ceSequence Analysismeganiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/megan
meme5.4.15.5.4memeTo updatememe_fimomeme_fimoSequence motif discovery, Nucleic acid feature detection, Protein feature detection, Statistical calculationSequence analysis, Genetic variation, Statistics and probability, Data miningThe MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses.A software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices.To updatehttp://meme-suite.org/ChIP-seqmemeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/meme
meme_chip4.11.21.3.26graphicsmagickTo updatePerforms motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.To updatehttp://meme-suite.org/ChIP-seqmeme_chipiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip
meningotype0.8.50.8.5meningotypeUp-to-dateAssign sequence type to N. meningitidis genome assembliesUp-to-datehttps://github.com/MDU-PHL/meningotypeSequence Analysismeningotypeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype
merlin1.1.21.1.2merlinUp-to-datemerlinMerlinHaplotype mapping, Genetic mappingGWAS study, MappingPedigree Analysis packageCan be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulationUp-to-datehttp://csg.sph.umich.edu/abecasis/Merlin/Variant Analysismerliniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/
merqury1.31.3merquryUp-to-datemerquryMerquryGenome assembly, k-mer counting, Scaffolding, Phasing, De-novo assemblySequence assembly, Whole genome sequencing, Plant biologyMerqury is a tool for evaluating genomes assemblies based of k-mer operations.Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.Up-to-datehttps://github.com/marbl/merquryAssemblymerquryiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury
meryl1.31.3merquryUp-to-dateMeryl a k-mer counter.Up-to-datehttps://github.com/marbl/merylAssemblymeryliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl
metabat22.152.15metabat2Up-to-dateMetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.Up-to-datehttps://bitbucket.org/berkeleylab/metabat/src/master/Metagenomicsmetabat2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/
metaeuk5.34c21f26.a5d39d9metaeukTo updateMetaEukMetaEukHomology-based gene predictionMetagenomics, Gene and protein familiesMetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand.MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomicsTo updatehttps://github.com/soedinglab/metaeukSequence Analysis, Genome annotationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk
metagenomeseq1.16.0-0.0.11.42.0bioconductor-metagenomeseqTo updatemetagenomeseqmetagenomeSeqSequence visualisation, Statistical calculationMetagenomics, SequencingmetagenomeSeq NormalizationDesigned to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.To updateMetagenomicsmetagenomeseq_normalizationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq
metaphlan4.0.64.0.6metaphlanUp-to-datemetaphlanMetaPhlAnNucleic acid sequence analysis, Phylogenetic tree analysisMetagenomics, PhylogenomicsMetaPhlAn for Metagenomic Phylogenetic AnalysisComputational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.Up-to-datehttps://github.com/biobakery/MetaPhlAnMetagenomicsmetaphlaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/
migmap1.0.31.0.3migmapUp-to-dateMiGMAPMiGMAPSequence analysis, Read mappingImmunoproteins, genes and antigens, Sequence analysismapper for full-length T- and B-cell repertoire sequencingMapper for full-length T- and B-cell repertoire sequencing.Up-to-datehttps://github.com/mikessh/migmapRNA, Sequence Analysismigmapiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap
minia3.2.63.2.6miniaUp-to-dateminiaMiniaGenome assemblySequence assemblyShort-read assembler based on a de Bruijn graphShort-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.Up-to-datehttps://gatb.inria.fr/software/minia/Assemblyminiaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/minia
miniasm0.3_r1790.3miniasmTo updateMiniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)To updatehttps://github.com/lh3/miniasmAssemblyminiasmiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm
minimap22.262.26minimap2Up-to-dateminimap2Minimap2Pairwise sequence alignmentMappingA fast pairwise aligner for genomic and spliced nucleotide sequencesPairwise aligner for genomic and spliced nucleotide sequencesUp-to-datehttps://github.com/lh3/minimap2Next Gen Mappersminimap2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2
miniprot0.120.12miniprotUp-to-dateAlign a protein sequence against a genome with affine gap penalty, splicing and frameshift.Up-to-datehttps://github.com/lh3/miniprotSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot
mirnature1.11.1mirnatureUp-to-dateComputational detection of canonical microRNAsUp-to-datehttps://github.com/Bierinformatik/miRNAtureRNA, Sequence Analysismirnatureiuchttps://github.com/Bierinformatik/miRNAture
mitobim1.9.11.9.1mitobimUp-to-dateassemble mitochondrial genomesUp-to-datehttps://github.com/chrishah/MITObimAssemblymitobimiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim
mitos1.1.12.1.3mitosTo updatemitosMITOSGenome annotationZoology, Whole genome sequencingde-novo annotation of metazoan mitochondrial genomesDe novo metazoan mitochondrial genome annotation.To updatehttp://mitos.bioinf.uni-leipzig.de/Sequence Analysismitosiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos
mlst2.22.02.23.0mlstTo updatemlstMLSTTaxonomic classificationImmunoproteins, genes and antigensScan contig files against PubMLST typing schemesMulti Locus Sequence Typing from an assembled genome or from a set of reads.To updatehttps://github.com/tseemann/mlstSequence Analysismlstiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst
moabs1.3.4.61.3.9.0moabsTo updateMOABS for differential methylation analysis on Bisulfite sequencing data.To updatehttps://github.com/sunnyisgalaxy/moabsEpigeneticsmoabsiuchttps://github.com/sunnyisgalaxy/moabs
mosdepth0.3.40.3.5mosdepthTo updatefast and flexible BAM/CRAM depth calculationTo updatehttps://github.com/brentp/mosdepthSAMmosdepthiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth
mothur1.01.48.0mothurTo updateMothur wrappersTo updatehttps://www.mothur.orgMetagenomicsmothuriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur
msaboot0.1.20.1.2msabootUp-to-dateA multiple sequences alignment bootstrapping tool.Up-to-datehttps://github.com/phac-nml/msabootFasta Manipulationmsabootiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot
multigps0.74.0fonts-conda-ecosystemTo updateAnalyzes collections of multi-condition ChIP-seq data.To updatehttp://mahonylab.org/software/multigps/ChIP-seqmultigpsiuc
multigsea1.8.01.10.0bioconductor-multigseaTo updatemultiGSEAmultiGSEAGene-set enrichment analysis, Aggregation, Pathway analysisMetabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small moleculesGSEA-based pathway enrichment analysis for multi-omics dataA GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.To updatehttps://bioconductor.org/packages/devel/bioc/html/multiGSEA.htmlTranscriptomics, Proteomics, Statisticsmultigseaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea
multiqc1.111.17multiqcTo updatemultiqcMultiQCValidationSequencing, BioinformaticsMultiQC aggregates results from bioinformatics analyses across many samples into a single reportMultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.To updatehttp://multiqc.info/Fastq Manipulation, Statistics, Visualizationmultiqciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc
mummer44.0.0rc14.0.0rc1mummer4Up-to-datemumer4MUMmer4Multiple sequence alignmentSequence analysis, Human geneticsMummer4 ToolsSystem for rapidly aligning large DNA sequences to one another.Up-to-datehttps://github.com/mummer4/mummerSequence Analysismummer4iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4
mykrobe0.10.00.13.0mykrobeTo updateMykrobeMykrobeAntimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimmingWhole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, MetagenomicsAntibiotic resistance predictionsAntibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installedTo updatehttps://github.com/Mykrobe-tools/mykrobeSequence Analysismykrobeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe
mzmine3.6.03.9.0mzmineTo updatemzmineMZmineNatural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generationProteomics, Metabolomics, Proteomics experiment, Small moleculesmass-spectrometry data processing, with the main focus on LC-MS dataToolbox for visualization and analysis of LC-MS data in netCDF or mzXML.To updatehttp://mzmine.github.io/Metabolomicsmzmine_batchiuchttps://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/
naltorfs0.1.20.1.2naltorfsUp-to-datenAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)Up-to-datehttps://github.com/BlankenbergLab/nAltORFsSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/
nanocompore1.0.0rc3.post21.0.4nanocomporeTo updateNanocomporeNanocomporePost-translation modification site prediction, PolyA signal detection, Genotyping, k-mer countingFunctional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sitesNanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitroTo updatehttps://nanocompore.rna.rocks/Sequence Analysisnanocomporeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore
nanoplot1.41.01.42.0nanoplotTo updatePlotting tool for long read sequencing data and alignmentsTo updatehttps://github.com/wdecoster/NanoPlotVisualizationnanoplotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/
nanopolishcomp0.6.110.6.12nanopolishcompTo updateNanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.To updatehttps://a-slide.github.io/NanopolishCompSequence Analysisnanopolishcompiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp
ncbi_acc_download0.2.80.2.8ncbi-acc-downloadUp-to-dateDownload sequences from GenBank/RefSeq by accession through the NCBI ENTREZ APIUp-to-datehttps://github.com/kblin/ncbi-acc-downloadData Sourcencbi_acc_downloadiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download
ncbi_datasets15.19.1ncbi-datasets-cliTo updatencbi_datasetsNCBI DatasetsData handling, Sequence database search, Data retrievalBiological databasesNCBI datasets downloads biological sequence data across all domains of life from NCBI.NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.To updatehttps://github.com/ncbi/datasetsData Sourcencbi_datasetsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets
ncbi_entrez_direct16.216.2entrez-directUp-to-dateNCBI Entrez Direct allow fetching data from NCBI DatabasesUp-to-datehttp://www.ncbi.nlm.nih.gov/books/NBK179288/Data Sourcencbi_entrez_directiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct
ncbi_entrez_eutils1.70pythonTo updateNCBI Entrez E-Utilties allow fetching data from NCBI DatabasesTo updatehttps://www.ncbi.nlm.nih.gov/books/NBK25501/Data Sourcencbi_entrez_eutilsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils
necat0.0.1_update202008030.0.1_update20200803necatUp-to-datenecatNECATDe-novo assemblySequence assemblyError correction and de-novo assembly for ONT Nanopore readsNECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.Up-to-datehttps://github.com/xiaochuanle/NECATAssemblynecatiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/necat
newick_utils1.6+galaxy11.6newick_utilsTo updatenewick_utilitiesNewick UtilitiesPhylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstructionPhylogeny, Genomics, Computer sciencePerform operations on Newick treesThe Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.To updatehttp://cegg.unige.ch/newick_utilsVisualization, Metagenomicsnewick_utilsiuchttps://github.com/tjunier/newick_utils
nextclade2.7.02.14.0nextalignTo updateIdentify differences between your sequences and a reference sequence used by NextstrainTo updatehttps://github.com/nextstrain/nextcladeSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade
ngmlr0.2.70.2.7ngmlrUp-to-datengmlrNGMLRDNA mapping, Sequence alignment, Genetic variation analysisSequencing, Mapping, DNA structural variationCoNvex Gap-cost alignMents for Long ReadsAn algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.Up-to-datehttps://github.com/philres/ngmlrNext Gen Mappersngmlriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr
ngsutils0.5.9ngsutilsTo updatengsutilsNGSUtilsRead pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filteringGenomics, TranscriptomicsNGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed.NGSUtils is a suite of software tools for working with next-generation sequencing datasetsTo updatehttps://github.com/ngsutils/ngsutilsSAMiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils
nonpareil3.1.13.4.1nonpareilTo updateEstimate average coverage in metagenomic datasetsTo updatehttp://nonpareil.readthedocs.ioMetagenomicsnonpareiliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil
novoplasty4.3.14.3.3novoplastyTo updateNOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.To updatehttps://github.com/ndierckx/NOVOPlastyAssemblynovoplastyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty
nugen_nudup2.3.32.3.3nudupUp-to-dateMarks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.Up-to-datehttp://nugentechnologies.github.io/nudup/SAM, Metagenomics, Sequence Analysis, Transcriptomicsnugen_nudupiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup
obitools1.2.131.2.13obitoolsUp-to-dateobitoolsOBIToolsSequence analysis, Sequence analysisSequence analysis, DNA, SequencingOBITools is a set of programs developed to simplify the manipulation of sequence filesSet of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.Up-to-datehttp://metabarcoding.org/obitoolsSequence Analysisobitoolsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools
ococo0.1.2.60.1.2.4ococoTo updateVariant detection of SNVsTo updatehttps://github.com/karel-brinda/ococoVariant Analysisococoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo
odgi0.30.8.3odgiTo updateRepresenting large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.To updatehttps://github.com/vgteam/odgiSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/
ont_fast5_api3.1.34.1.1ont-fast5-apiTo updateont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.To updatehttps://github.com/nanoporetech/ont_fast5_api/Nanoporeont_fast5_apiiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api
onto_toolkit1.451.45perl-onto-perlUp-to-dateONTO-Toolkit is a collection of tools for managing ontologies.Up-to-datehttp://search.cpan.org/~easr/ONTO-PERL-1.45/Ontology Manipulationonto_toolkitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit
optdoev2.0.2doebaseTo updateOptimal Design Of ExperimentTo updatehttps://github.com/pablocarb/doebaseSynthetic Biologyoptdoeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe
optitype1.3.51.3.5optitypeUp-to-datePrecision HLA typing from NGS dataUp-to-datehttps://github.com/FRED-2/OptiTypeSequence Analysisoptitypeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1
orfipy0.0.40.0.4orfipyUp-to-dateorfipyorfipyCoding region prediction, Database search, Transcriptome assembly, De-novo assemblyComputer science, RNA-Seq, Transcriptomics, Small moleculesGalaxy wrapper for ORFIPYA fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.Up-to-datehttps://github.com/urmi-21/orfipySequence Analysisorfipyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy
orthofinder2.5.42.5.5orthofinderTo updateOrthoFinderOrthoFinderGenome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignmentPhylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysisAccurate inference of orthologous gene groups made easyOrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.To updatehttps://github.com/davidemms/OrthoFinderPhylogenetics, Sequence Analysisorthofinderiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder
packaged_annotation_loader0.1pythonTo updateTool to make cached genome annotation data available as a list of datasets collectionTo updateData Sourcepackaged_annotation_loaderiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader
pangolin4.34.3pangolinUp-to-datePangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.Up-to-datehttps://github.com/cov-lineages/pangolinSequence Analysispangoliniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin
parse_mito_blast1.0.21.0.2parse_mito_blastUp-to-dateFiltering blast out from querying assembly against mitochondrial database.Up-to-datehttps://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.pySequence Analysisparse_mito_blastiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast
pathview1.34.01.40.0bioconductor-pathviewTo updatepathviewpathviewPathway or network analysis, Pathway or network visualisationMolecular interactions, pathways and networks, Systems biology, Data visualisationPathview is a tool set for pathway based data integration and visualization.Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.To updatehttps://bioconductor.org/packages/release/bioc/html/pathview.htmlStatistics, RNA, Micro-array Analysispathviewiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview
pbgcpp2.0.22.0.2pbgcppUp-to-dategenomicconsensusGenomicConsensusVariant callingMappingCompute genomic consensus and call variants using PacBio reads mapped to a referenceThe GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.Up-to-datehttps://github.com/PacificBiosciences/gcppVariant Analysispbgcppiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp
pbmm21.10.01.13.0pbmm2To updatepbmm2pbmm2Pairwise sequence alignment, SortingMappingA minimap2 SMRT wrapper for PacBio data.pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.To updatehttps://github.com/PacificBiosciences/pbmm2Next Gen Mapperspbmm2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2
pe_histogram1.0.1openjdkTo updateContains a tool that produces an insert size histogram for a paired-end BAM file.To updatehttps://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogramGraphicspe_histogramiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram
pear0.9.60.9.6pearUp-to-datepearPEARSequence mergingSequence assemblyPEAR evaluates all possible paired-end read overlapsPaired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.Up-to-datepeariuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pear
pharokka1.3.2\n pharokka\nTo update\n pharokka\nrapid standardised annotation tool for bacteriophage genomes and metagenomesTo updatehttps://github.com/gbouras13/pharokkaGenome annotationpharokkaiuchttps://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka
phyloseq1.38.01.44.0bioconductor-phyloseqTo updateHandling and analysis of high-throughput microbiome census dataTo updatehttps://www.bioconductor.org/packages/release/bioc/html/phyloseq.htmlMetagenomicsphyloseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq
phyml3.3.202204083.3.20220408phymlUp-to-datephymlPhyMLPhylogenetic tree generation (maximum likelihood and Bayesian methods)Phylogenetics, Bioinformatics, PhylogeneticsPhyML is a phylogeny software based on the maximum-likelihood principle.Phylogenetic estimation software using Maximum LikelihoodUp-to-datehttp://www.atgc-montpellier.fr/phyml/Phylogeneticsphymliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml
picard2.18.23.1.0picardTo updatepicard_fastqtosampicard_fastqtosamFormattingSequencingPicard SAM/BAM manipulation tools.Create an unaligned BAM file.To updatehttp://broadinstitute.github.io/picard/SAMpicarddevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/picard
picrust1.1.11.1.4picrustTo updatePICRUSt wrappersTo updatehttps://picrust.github.io/picrust/Metagenomicspicrustiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust
picrust22.5.12.5.2picrust2To updatepicrust2PICRUSt2Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysisMetagenomics, Microbiology, Phylogenetics, Metagenomic sequencingPICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved StatesPICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.To updatehttps://github.com/picrust/picrust2/wikiMetagenomicspicrust2iuchttps://github.com/picrust/picrust2
pilon1.20.11.24pilonTo updatepilonpilonSequence assembly, Analysis, Read alignmentAssemblypilon is a tool for assembly improvement and variant analysis in bacteriaRead alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.To updateVariant Analysispiloniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon
pipelign0.20.2pipelignUp-to-dateMultipe sequence alignmentUp-to-datehttps://github.com/asmmhossain/pipelign/Next Gen Mapperspipeligniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign
pizzly0.37.3.10.37.3pizzlyTo updatePizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.To updatehttps://github.com/pmelsted/pizzly/Transcriptomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/
plasflow1.1.01.1.0plasflowUp-to-datePlasFlow - Prediction of plasmid sequences in metagenomic contigs.Up-to-datehttps://github.com/smaegol/PlasFlowSequence Analysisplasflowiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow
plasmidfinder2.1.62.1.6plasmidfinderUp-to-datePlasmidFinderPlasmidFinderGenome assembly, Scaffolding, Multilocus sequence typingWhole genome sequencing, Sequence assembly, Mapping, Probes and primers"PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).Up-to-datehttps://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/Sequence Analysisplasmidfinderiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder
plink1.90b6.211.90b6.21plinkUp-to-dateplinkPLINKGenetic variation analysisGWAS studyPLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.Up-to-datehttps://www.cog-genomics.org/plinkGenome-Wide Association Studyplinkiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/plink
polypolish0.5.00.5.0polypolishUp-to-datePolypolishPolypolishGenome assembly, Read mapping, Mapping assembly, Sequencing error detectionSequence assembly, Sequence composition, complexity and repeats, Mapping"Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.Up-to-datehttps://github.com/rrwick/PolypolishSequence Analysispolypolishiuchttps://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish
porechop0.2.4porechopTo updatePorechop - Finding and removing adapters from Oxford Nanopore readsTo updatehttps://github.com/rrwick/PorechopFasta Manipulation, Fastq Manipulationporechopiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop
poretools0.6.1a10.6.1a1poretoolsUp-to-dateporetoolsPoretoolsNucleic acid sequence analysisDNA, SequencingA flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.Up-to-datehttps://poretools.readthedocs.io/en/latest/Fasta Manipulation, Fastq Manipulationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools
presto0.6.20.7.1prestoTo updateprestopRESTONucleic acid sequence analysisSequencing, DNA, ImmunologypRESTO toolkit for immune repertoire analysis.Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.To updatehttps://presto.readthedocs.io/Sequence Analysisprestoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/presto
pretext0.1.90.1.9pretextmapUp-to-dateProcess genome contacts maps processing images.Up-to-datehttps://github.com/wtsi-hpag/PretextSnapshotSequence Analysissuite_pretextiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext
prinseq@TOOL_VERSION+galaxy20.20.4prinseqTo updateprinseqPRINSEQRead pre-processing, Sequence trimming, Sequence contamination filteringTranscriptomics, Metagenomics, GenomicsPRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasetsPRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.To updatehttp://prinseq.sourceforge.net/manual.htmlFastq Manipulation, Metagenomicsprinseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/
progressivemauvesnapshot_2015_02_13progressivemauveTo updateMauve/ProgressiveMauve Multiple Sequence AlignerTo updateSequence Analysisprogressivemauveiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve
prokka1.14.61.14.6prokkaUp-to-dateprokkaProkkaGene prediction, Coding region prediction, Genome annotationGenomics, Model organisms, VirologyRapid annotation of prokaryotic genomesSoftware tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.Up-to-datehttp://github.com/tseemann/prokkaSequence Analysisprokkacrs4https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/
prot-scriber0.1.40.1.4prot-scriberUp-to-dateProtein annotation of short human readable descriptionsUp-to-datehttps://github.com/usadellab/prot-scriberProteomicsprot_scriberiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber
proteinortho6.2.36.3.0proteinorthoTo updateproteinorthoProteinorthoHomology-based gene predictionPhylogenyProteinortho is a tool to detect orthologous proteins/genes within different species.Proteinortho is a tool to detect orthologous genes within different speciesTo updatehttps://gitlab.com/paulklemm_PHD/proteinorthoProteomicsproteinorthoiuchttps://gitlab.com/paulklemm_PHD/proteinortho
psiclass1.0.31.0.3psiclassUp-to-datepsiclassPsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.Up-to-datehttps://github.com/splicebox/PsiCLASSTranscriptomicspsiclassiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass
pureclip1.0.41.3.1pureclipTo updatePureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP dataTo updatehttps://github.com/skrakau/PureCLIPSequence Analysis, RNA, CLIP-seqpureclipiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip
purge_dups1.2.61.2.6purge_dupsUp-to-datepurge_dupspurge_dupsGenome assembly, Read binning, ScaffoldingSequence assemblyPurge haplotigs and overlaps in an assembly based on read depthIdentifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuencesUp-to-datehttps://github.com/dfguan/purge_dupsAssemblypurge_dupsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups
pycoqc2.5.22.5.2pycoqcUp-to-dateQC metrics for ONT BasecallingUp-to-datehttps://github.com/tleonardi/pycoQCNanoporepycoqciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc
pyega35.0.25.1.0pyega3To updateEGA python client uses the EGA REST API to download authorized datasets and files.To updatehttps://github.com/EGA-archive/ega-download-clientData Sourceega_download_clientiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3
pygenometracks3.83.8pygenometracksUp-to-datepyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.Up-to-datehttps://github.com/deeptools/pyGenomeTracksVisualizationpygenometracksiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks
pysradb1.4.22.2.0pysradbTo updatepysradbpysradbDeposition, Data retrievalSequencing, Gene transcripts, Bioinformaticspysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.To updatehttps://github.com/saketkc/pysradbSequence Analysispysradb_searchiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb
qfilt1.0.0+galaxy10.0.1qfiltTo updateFilter sequencing dataTo updatehttps://github.com/veg/qfiltFastq Manipulationqfiltiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt
qiime_add_on1.9.1qiimeTo updateQIIME to perform microbial community analysisTo updatehttp://www.qiime.orgMetagenomicsqiimeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/
qiime_core1.9.1qiimeTo updateQIIME to perform microbial community analysisTo updatehttp://www.qiime.orgMetagenomicsqiimeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/
qq_tools0.1.00.1.4r-qqmanTo updateTo updatehttps://CRAN.R-project.org/package=qqmanVisualization, Variant Analysisiuc
qualimap2.2.2d2.2.2dqualimapUp-to-datequalimapQualiMapSequencing quality controlData quality managementPlatform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.Up-to-datehttp://qualimap.bioinfo.cipf.es/Sequence Analysis, Transcriptomics, SAMqualimapiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap
quast5.2.05.2.0quastUp-to-datequastQUASTVisualisation, Sequence assembly validationSequence assemblyQuast (Quality ASsessment Tool) evaluates genome assemblies.QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.Up-to-datehttp://quast.bioinf.spbau.ru/Assemblyquastiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/quast
query_impc0.9.0requestsTo updateContains a tool to query the IMPC database.To updatehttps://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impcConvert Formats, Web Servicesquery_impciuchttps://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc
query_tabular3.3.0pythonTo updateLoads tabular files into a SQLite DB to perform a SQL query producing a tabular outputTo updateText Manipulationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular
quickmerge0.30.3quickmergeUp-to-datequickmergequickmergeGenome assembly, Scaffolding, De-novo assembly, GenotypingStructural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotypeMerge long-read and hybrid assemblies to increase contiguityQuickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.Up-to-datehttps://github.com/mahulchak/quickmergeAssemblyquickmergegalaxy-australiahttps://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge
raceid0.2.30.1.3r-raceidTo updateRaceID3, StemID2, FateID - scRNA analysisTo updatehttps://github.com/dgrun/RaceID3_StemID2_package/Transcriptomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3
ragtag2.1.02.1.0ragtagUp-to-dateragtagragtagGenome assemblySequence assemblyReference-guided scaffolding of draft genomes tool.RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.Up-to-datehttps://github.com/malonge/RagTagAssemblyragtagiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag
rapidnj2.3.22.3.2rapidnjUp-to-daterapidnjRapidNJPhylogenetic tree generationPhylogenyGalaxy wrapper for the RapidNJ toolA tool for fast canonical neighbor-joining tree construction.Up-to-datehttps://birc.au.dk/software/rapidnj/Phylogeneticsrapidnjiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj
raven1.8.01.8.3raven-assemblerTo updateRaven is a de novo genome assembler for long uncorrected reads.To updatehttps://github.com/lbcb-sci/ravenAssemblyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/raven
raxml8.2.128.2.13raxmlTo updateraxmlRAxMLSequence analysis, Phylogenetic tree analysisPhylogenetics, Sequence analysisRAxML - A Maximum Likelihood based phylogenetic inferenceA tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.To updatehttp://www.exelixis-lab.org/web/software/raxml/Phylogeneticsraxmliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml
rcorrector1.0.3+galaxy11.0.6rcorrectorTo updatercorrectorRcorrectorSequencing error detectionRNA, RNA-Seq, SequencingRcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.To updatehttps://github.com/mourisl/RcorrectorFastq Manipulationrcorrectoriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector
read_it_and_keep0.2.20.3.0read-it-and-keepTo updateRapid decontamination of SARS-CoV-2 sequencing readsTo updatehttps://github.com/GenomePathogenAnalysisService/read-it-and-keepSequence Analysisread_it_and_keepiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep
recentrifuge1.12.11.12.1recentrifugeUp-to-dateRecentrifugeRecentrifugeTaxonomic classification, Expression analysis, Cross-assemblyMetagenomics, Microbial ecology, Metagenomic sequencing"With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."Robust comparative analysis and contamination removal for metagenomics.Up-to-datehttps://github.com/khyox/recentrifugeMetagenomicsrecentrifugeiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge
red2018.09.102018.09.10redUp-to-dateRed (REpeat Detector)Up-to-datehttps://github.com/BioinformaticsToolsmith/RedSequence Analysisrediuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/red
repeatmasker4.1.54.1.5repeatmaskerUp-to-daterepeatmaskerRepeatMaskerGenome annotationSequence analysis, Sequence composition, complexity and repeatsRepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).Up-to-datehttp://www.repeatmasker.org/Sequence Analysisrepeat_maskerbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker
repeatmodeler2.0.4To updateRepeatModeler - Model repetitive DNATo updatehttps://www.repeatmasker.org/RepeatModeler/Genome annotationrepeatmodelercsblhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler
repmatch_gff3matplotlibTo updateContains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria.To updateChIP-seqrepmatch_gff3iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3
reshape21.4.2r-reshape2To updateFlexibly restructure and aggregate data using just the two functions melt and dcastTo updatehttps://cran.r-project.org/web/packages/reshape2/index.htmlText Manipulationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2
resize_coordinate_window1.0.2pythonTo updateContains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size.To updateGenomic Interval Operationsresize_coordinate_windowiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window
rgcca3.0.23.0.3rgccacmdTo updatemulti-block analysisTo updatehttps://github.com/rgcca-factory/RGCCAStatisticsrgccaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca
rgrnastar2.7.10b2.7.11astarTo updatestarSTARSequence alignmentRNA-Seq, TranscriptomicsRNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapperUltrafast universal RNA-seq data alignerTo updatehttps://github.com/alexdobin/STARNext Gen Mappers, Transcriptomicsrgrnastariuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar
ribowaltz1.2.01.2.0ribowaltzUp-to-dateriboWaltzriboWaltzComputational biologyCalculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling datariboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.Up-to-datehttps://github.com/LabTranslationalArchitectomics/riboWaltzTranscriptomics, RNAiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz
rnaquast2.2.32.2.3rnaquastUp-to-daternaQUASTrnaQUASTDe-novo assembly, Transcriptome assembly, Sequence assembly validationSequence assembly, Transcriptomics, RNA-seqrnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.Quality assessment tool for de novo transcriptome assemblies.Up-to-datehttps://github.com/ablab/rnaquastAssembly, RNArnaquastiuchttps://git.ufz.de/lehmanju/rnaquast
roary3.13.03.13.0roaryUp-to-dateroaryRoaryGenome assemblyDNA, Genomics, MappingRoary the pangenome pipelineA high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.Up-to-datehttps://sanger-pathogens.github.io/Roary/Sequence Analysisroaryiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/roary
rp2biosensor3.2.1rp2biosensorTo updateBuild Sensing-Enabling Metabolic Pathways from RetroPath2.0 outputTo updatehttps://github.com/brsynth/rp2biosensorSynthetic Biologyrp2biosensoriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor
rp2paths1.5.0rp2pathsTo updateEnumerate and seperate the different pathways generated by RetroPath2.0To updatehttps://github.com/brsynth/rp2pathsSynthetic Biologyrp2pathsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths
rpbasicdesign1.1.1rpbasicdesignTo updateExtracting enzyme IDs from rpSBML filesTo updatehttps://github.com/brsynth/rpbasicdesignSynthetic Biologyrpbasicdesigniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign
rpfba5.12.3rptoolsTo updatePerform FBA for the RetroPath2.0 heterologous pathwaysTo updatehttps://github.com/brsynth/rptools/releasesSynthetic Biologyrpfbaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba
rptools5.13.1rptoolsTo updateSuite of tools that work on rpSBML formatTo updatehttps://github.com/brsynth/rptoolsSynthetic Biologyrptoolsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools
rrparser2.5.2rrparserTo updateReaction Rules ParserTo updatehttps://github.com/brsynth/RRParserSynthetic Biologyrrparseriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser
rseqc5.0.15.0.3rseqcTo updaterseqcRSeQCData handlingSequencingan RNA-seq quality control packageProvides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.To updatehttps://code.google.com/p/rseqc/Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualizationrseqcnileshhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc
ruvseq1.26.01.34.0bioconductor-ruvseqTo updateruvseqRUVSeqDifferential gene expression analysisGene expression, RNA-seqRemove Unwanted Variation from RNA-Seq DataThis package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.To updatehttps://www.bioconductor.org/packages/release/bioc/html/DESeq2.htmlTranscriptomics, RNA, Statisticsruvseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq
salsa22.32.3salsa2Up-to-dateSALSASALSAGenome assembly, De-novo assembly, ScaffoldingSequence assembly, DNA binding sites, MappingA tool to scaffold long read assemblies with Hi-C> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branchUp-to-datehttps://github.com/marbl/SALSAAssemblysalsaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2
samblaster0.1.240.1.26samblasterTo updatesamblasterSAMBLASTERSplit read mappingDNA, Sequencing, Mappingsamblaster marks duplicates and can output split and discordant alignments from SAM/BAM filesA tool to mark duplicates and extract discordant and split reads from SAM files.To updatehttps://github.com/GregoryFaust/samblasterSAM, Fastq Manipulation, Variant Analysissamblasteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster
sansa0.0.80.0.8sansaUp-to-dateSansa is a tool for structural variant annotation.Up-to-datehttps://github.com/dellytools/sansaVariant Analysissansaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa
sarscov2formatter1.01.0sarscov2formatterUp-to-datesarscov2formatter custom scriptUp-to-datehttps://github.com/nickeener/sarscov2formatterSequence Analysissarscov2formatteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter
sarscov2summary0.10.5sarscov2summaryTo updatesarscov2summary custom scriptTo updatehttps://github.com/nickeener/sarscov2summarySequence Analysissarscov2summaryiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary
sbml2sbol0.1.13sbml2sbolTo updateConvert SBML to SBOL formatTo updatehttps://github.com/neilswainston/SbmlToSbolSynthetic Biologysbml2sboliuc
scanpy@galaxy_version@1.7.2scanpyTo updatescanpySCANPYDifferential gene expression analysisGene expression, Cell biology, GeneticsScanpy – Single-Cell Analysis in PythonScalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.To updatehttps://scanpy.readthedocs.ioTranscriptomics, Sequence Analysisscanpyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/
scater1.22.01.28.0bioconductor-scaterTo updatescaterscaterRead pre-processing, Sequencing quality control, Sequence visualisationRNA-seq, Quality affairs, Molecular geneticsScater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.To updatehttp://bioconductor.org/packages/scater/Transcriptomics, RNA, Visualizationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/scater
schicexplorer47schicexplorerTo updatescHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.To updatehttps://github.com/joachimwolff/schicexplorerSequence Analysis, Transcriptomics, Visualizationschicexploreriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer
scikit-bio0.4.20.4.2scikit-bioUp-to-datescikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformaticsUp-to-datehttp://scikit-bio.org/Sequence Analysisscikit_bioiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio
scoary1.6.161.6.16scoaryUp-to-dateScoary calculates the assocations between all genes in the accessory genome and the traits.Up-to-datehttps://github.com/AdmiralenOla/ScoaryMetagenomicsscoaryiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary
scpipe1.0.0+galaxy22.0.0bioconductor-scpipeTo updatescpipescPipeGenome annotation, Validation, Alignment, VisualisationGene expression, RNA-seq, SequencingA flexible preprocessing pipeline for single-cell RNA-sequencing dataA preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.To updatehttp://bioconductor.org/packages/release/bioc/html/scPipe.htmlTranscriptomics, RNA, Statisticsscpipeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe
seacr1.31.3seacrUp-to-dateSEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes.Up-to-datehttps://github.com/FredHutch/SEACREpigenetics, ChIP-seqseacriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr
selenzy_wrapper0.3.00.3.0selenzy_wrapperUp-to-datePerforms enzyme selection from a reaction query.Up-to-datehttps://github.com/brsynth/selenzy-wrapperSynthetic Biologyselenzy_wrapperiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper
semibin1.5.12.0.2semibinTo updatesemibinSemiBinSequence assembly, Read binning, VisualisationMetagenomics, Machine learning, Microbial ecology, Sequence assemblySemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural NetworksCommand tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.To updatehttps://semibin.readthedocs.io/en/latest/Metagenomicssemibiniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin
seq2hla2.32.3seq2hlaUp-to-dateseq2hlaSeq2HLARead mapping, Genetic variation analysisTranscriptomics, MappingPrecision HLA typing and expression from RNAseq dataseq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.Up-to-datehttps://github.com/TRON-Bioinformatics/seq2HLASequence Analysisseq2hlaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla
seqcomplexity0.1.20.1.2seqcomplexityUp-to-dateSequence complexity for raw readsUp-to-datehttps://github.com/stevenweaver/seqcomplexitySequence Analysisiuchttps://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/
seqkit2.3.12.5.1seqkitTo updateseqkitseqkitDNA transcription, Sequence trimming, DNA translation, Sequence conversionDatabase management, Sequence analysisA cross-platform and ultrafast toolkit for FASTA/Q file manipulationFASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.To updatehttps://bioinf.shenwei.me/seqkit/Sequence Analysisseqkitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit
seqtk1.31.4seqtkTo updateseqtkseqtkData handling, Sequence file editingData managementToolkit for processing sequences in FASTA/Q formatsA tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.To updatehttps://github.com/lh3/seqtkSequence Analysisseqtkiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk
seqwish0.7.50.7.9seqwishTo updateAlignment to variation graph inducerTo updatehttps://github.com/ekg/seqwishSequence Analysis, Variant Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/
seurat4.3.0.13.0.2r-seuratTo updateA toolkit for quality control, analysis, and exploration of single cell RNA sequencing dataTo updatehttps://github.com/satijalab/seuratTranscriptomics, RNA, Statisticsseuratiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat
shasta0.6.00.11.1shastaTo updateFast de novo assembly of long read sequencing dataTo updatehttps://github.com/chanzuckerberg/shastaAssembly, Nanoporeshastaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta
shorah1.1.31.99.2shorahTo updateshorahShoRAHHaplotype mapping, Variant callingMetagenomics, Sequencing, GeneticsReconstruct haplotypes using ShoRAH in amplicon modeInference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.To updatehttps://github.com/cbg-ethz/shorah/blob/master/README.mdSequence Analysisshorah_ampliconiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah
shovill1.1.01.1.0shovillUp-to-dateshovillshovillGenome assemblyGenomics, Microbiology, Sequence assemblyFaster de novo assembly pipeline based around SpadesShovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.Up-to-datehttps://github.com/tseemann/shovillAssemblyshovilliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill
sickle1.33.21.33sickle-trimTo updatesicklesickleSequence trimmingData quality managementA windowed adaptive trimming tool for FASTQ files using qualityA tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.To updatehttps://github.com/najoshi/sickleFastq Manipulation, Sequence Analysissickleiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle
simtext0.0.21.0.1r-argparseTo updateA text mining framework for interactive analysis and visualization of similarities among biomedical entities.To updatehttps://github.com/dlal-group/simtextText Manipulationsimtextiuchttps://github.com/galaxyproject/tools-iuc/tools/simtext
sina1.7.21.7.2sinaUp-to-datesinaSINASequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignmentSequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, TaxonomySINA reference based multiple sequence alignmentAligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignmentUp-to-datehttps://sina.readthedocs.io/en/latest/Sequence Analysissinaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sina
sinto0.9.00.10.0sintoTo updateSinto single-cell analysis toolsTo updatehttps://github.com/timoast/sintoSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto
slamdunk0.4.30.4.3slamdunkUp-to-dateSlamdunk maps and quantifies SLAMseq readsUp-to-datehttp://t-neumann.github.io/slamdunkRNA, Transcriptomics, Sequence Analysis, Next Gen Mappersslamdunkiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk
sleuth0.30.10.30.1r-sleuthUp-to-datesleuthsleuthExpression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculationRNA-seq, Gene expression, Statistics and probabilitySleuth is a program for differential analysis of RNA-Seq data.A statistical model and software application for RNA-seq differential expression analysis.Up-to-datehttps://github.com/pachterlab/sleuthTranscriptomics, RNA, Statisticssleuthiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth
smallgenomeutilities0.4.00.4.0smallgenomeutilitiesUp-to-datev-pipeV-pipeRead pre-processing, Sequence alignment, Genetic variation analysisGenomics, Population genetics, Workflows, Virology, SequencingSet of utilities for manipulating small viral genome data.Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.Up-to-datehttps://github.com/cbg-ethz/smallgenomeutilitiesSequence Analysissmallgenomeutilitiesiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities
smudgeplot0.2.50.2.5smudgeplotUp-to-datesmudgeplotsSmudgeplotsSequence trimming, Genotyping, k-mer countingSequence assembly, Genetic variation, MathematicsInference of ploidy and heterozygosity structure using whole genome sequencingReference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568Up-to-datehttps://github.com/KamilSJaron/smudgeplotAssemblysmudgeplotgalaxy-australiahttps://github.com/galaxyproject/tools-iuc
snap2013_11_292013_11_29snapUp-to-datesnapSNAPGene predictionDNA, DNA polymorphism, GeneticsSNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.Up-to-datehttps://github.com/KorfLab/SNAPSequence Analysissnapiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/snap
sniffles1.0.122.2snifflesTo updatesnifflesSnifflesSequence analysis, Structural variation detectionDNA structural variation, SequencingGalaxy wrapper for snifflesAn algorithm for structural variation detection from third generation sequencing alignment.To updatehttps://github.com/fritzsedlazeck/SnifflesSequence Analysissnifflesiuchttps://github.com/galaxyproject/tools-iuc
snipit1.0.71.1.2snipitTo updateSummarise snps relative to a reference sequenceTo updatehttps://github.com/aineniamh/snipitVariant Analysis, Sequence Analysissnipitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit
snippy4.6.0snippyTo updatesnippysnippyPhylogenetic tree visualisation, Phylogenetic tree generation, Variant callingGenomics, Model organisms, DNA polymorphism, PhylogeneticsContains the snippy tool for characterising microbial snpsRapid haploid variant calling and core SNP phylogeny generation.To updatehttps://github.com/tseemann/snippySequence Analysissnippyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy
snp-dists0.8.20.8.2snp-distsUp-to-dateCompute pairwise SNP distance matrix from a FASTA sequence alignmentUp-to-datehttps://github.com/tseemann/snp-distsVariant Analysissnp_distsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists
snp-sites2.5.12.5.1snp-sitesUp-to-dateFinds SNP sites from a multi-FASTA alignment fileUp-to-datehttps://github.com/sanger-pathogens/snp-sitesVariant Analysissnp_sitesiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites
snpeff-covid19To updatesnpeffsnpEffSNP detectionDNA polymorphism, Genetic variation, Nucleic acid sites, features and motifsSnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolboxVariant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).To updatehttp://snpeff.sourceforge.net/Genome-Wide Association Study, Variant Analysissnpeff_sars_cov_2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff
snpfreqplot1.0r-baseTo updateGenerates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 dataTo updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/Variant Analysissnpfreqplotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/
socru2.1.72.2.4socruTo updateOrder and orientation of complete bacterial genomesTo updatehttps://github.com/quadram-institute-bioscience/socruSequence Analysissocruiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/socru
sonneityping2021020120210201sonneitypingUp-to-dateScripts for parsing Mykrobe predict results for Shigella sonnei.Up-to-datehttps://github.com/katholt/sonneitypingSequence Analysissonneitypingiuchttps://github.com/katholt/sonneityping
spades3.15.53.15.5spadesUp-to-dateSPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.Up-to-datehttps://github.com/ablab/spadesAssembly, RNA, Metagenomicsspadesiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/spades
spaln2.4.9pythonTo updateSpaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.To updatehttp://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/Sequence Analysis, Genome annotationspalniuchttps://github.com/ogotoh/spaln
spotyping2.12.1spotypingUp-to-datespotypingSpoTypingVariant pattern analysisMicrobiology, Sequencing, Sequence composition, complexity and repeats, Genetic variationSpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence readsFast and accurate in silico Mycobacterium spoligotyping from sequence reads.Up-to-datehttps://github.com/xiaeryu/SpoTyping-v2.0Sequence Analysisspotypingiuchttps://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine
spyboat0.1.2spyboatTo updateWavelet analysis for 3d-image stacksTo updatehttp://github.com/tensionhead/spyboatImaging, Graphicsspyboatiuchttps://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat
sra-tools3.0.83.0.8sra-toolsUp-to-datesra-toolsSRA Software ToolkitData handlingDNA, Genomics, SequencingNCBI Sequence Read Archive toolkit utilitiesThe SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.Up-to-datehttps://github.com/ncbi/sra-toolsData Source, Fastq Manipulationsra_toolsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools
srst20.2.01.18samtoolsTo updateSRST2 Short Read Sequence Typing for Bacterial PathogensTo updatehttp://katholt.github.io/srst2/Metagenomicssrst2iuchttps://github.com/katholt/srst2
stacks2.65stacksTo updatestacksStacksData handlingMapping, Population geneticsStacks is a software pipeline for building loci from short-read sequences, such as RAD-seqDeveloped to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.To updatehttp://catchenlab.life.illinois.edu/stacks/Sequence Analysisstacksiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks
stacks22.552.65stacksTo updateStacks is a software pipeline for building loci from short-read sequences, such as RAD-seqTo updatehttp://catchenlab.life.illinois.edu/stacks/Sequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2
star_fusion0.5.4-3+galaxy11.12.0star-fusionTo updateSTAR Fusion detects fusion genes in RNA-Seq data after running RNA-STARTo updateSequence Analysis, Transcriptomicsstar_fusioniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion
straindesign3.2.23.2.2straindesignUp-to-dateToolbox to optimize biological modelUp-to-datehttps://github.com/brsynth/straindesignSystems Biology, Synthetic Biologystraindesigniuchttps://github.com/brsynth/straindesign
strelka2.9.102.9.10strelkaUp-to-dateUp-to-datehttps://github.com/Illumina/strelka/Variant Analysisstrelkaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka
stringtie2.2.12.2.1stringtieUp-to-datestringtieStringTieTranscriptome assembly, RNA-Seq analysisTranscriptomics, RNA-seqStringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.Up-to-datehttp://ccb.jhu.edu/software/stringtie/Transcriptomicsstringtieiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie
structure2.3.42.3.4structureUp-to-datestructureStructureGenetic variation analysisPopulation geneticsfor using multi-locus genotype data to investigate population structure.The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.Up-to-datePhylogenetics, Variant Analysisstructureiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/structure
structureharvester0.6.940.6.94structureharvesterUp-to-datefor parsing STRUCTURE outputs and for performing the Evanno methodUp-to-datePhylogenetics, Variant Analysisstructureharvesteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester
swift1.01.0swiftlinkUp-to-dateParallel MCMC Linkage AnalysisUp-to-datehttps://github.com/ajm/swiftlinkVariant Analysisswiftlinkiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/
syndiva1.01.2.4clustaloTo updateSynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.To updateProteomicssyndivaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA
table_compute1.2.4pandasTo updatePerform general-purpose table operationsTo updateText Manipulationtable_computeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute
tag_pileup_frequency1.0.2openjdkTo updateContains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file.To updatehttps://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileupStatistics, SAM, Genomic Interval Operationstag_pileup_frequencyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency
tasmanian_mismatch1.0.71.0.7tasmanian-mismatchUp-to-dateAnalysis of positional mismatchesUp-to-dateSequence Analysistasmanian_mismatchiuchttps://github.com/nebiolabs/tasmanian-mismatch
taxonomy_filter_refseq0.3.01.0.7rust-ncbitaxonomyTo updateFilter RefSeq by taxonomyTo updatehttps://github.com/pvanheus/ncbitaxonomySequence Analysis, Genome annotationtaxonomy_filter_refseqiuchttps://github.com/galaxyproject/tools-iuc
taxonomy_krona_chart2.7.1+galaxy02.8.1kronaTo updatekronaKronaVisualisationMetagenomicsKrona pie chart from taxonomic profileKrona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).To updatehttp://sourceforge.net/projects/krona/Assemblytaxonomy_krona_chartcrs4https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart
tb-profiler4.4.15.0.1tb-profilerTo updateProcesses M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.To updatehttps://github.com/jodyphelan/TBProfilerSequence Analysistbprofileriuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler
tb_variant_filter0.4.00.4.0tb_variant_filterUp-to-dateM. tuberculosis H37Rv VCF filterUp-to-datehttps://github.com/COMBAT-TB/tb_variant_filterVariant Analysistb_variant_filteriuchttps://github.com/COMBAT-TB/tb_variant_filter
tbl2gff31.20.6.6bcbiogffTo updateTable to GFF3To updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3Convert Formats, Sequence Analysistbl2gff3iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3
tbvcfreport0.1.100.1.10tbvcfreportUp-to-dateGenerate HTML report from SnpEff M.tuberculosis VCF(s)Up-to-datehttps://github.com/COMBAT-TB/tbvcfreportVariant Analysistbvcfreportiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport
te_finder1.0.11.18samtoolsTo updatetefinderTEfinderGenome indexing, Variant calling, PCR primer designSequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variationTransposable element insertions finderA Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.To updatehttps://github.com/VistaSohrab/TEfinderSequence Analysiste_finderiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/
telescope1.0.31.0.3telescopeUp-to-dateTelescope-expressionTelescopeEssential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mappingRNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assemblySingle locus resolution of Transposable ELEment expression.Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.Up-to-datehttps://github.com/mlbendall/telescope/Genome annotationtelescope_assigniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope
tetoolkit2.2.32.2.3tetranscriptsUp-to-dateThe TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.Up-to-datehttp://hammelllab.labsites.cshl.edu/software/Sequence Analysistetoolkitiuchttps://github.com/mhammell-laboratory/TEtranscripts
tetyper1.11.1tetyperUp-to-dateType a specific transposable element (TE) of interest from paired-end sequencing data.Up-to-datehttps://github.com/aesheppard/TETyperSequence Analysistetyperiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper
tn931.0.61.0.9tn93To updateCompute distances between sequencesTo updatehttps://github.com/veg/tn93/Sequence Analysistn93iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/
tracy0.6.10.7.5tracyTo updateTo updateiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy
transdecoder5.5.05.7.1transdecoderTo updateTransDecoderTransDecoderCoding region prediction, de Novo sequencing, De-novo assemblyGenomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencingTransDecoder finds coding regions within transcriptsTransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.To updatehttps://transdecoder.github.io/Transcriptomics, RNAtransdecoderiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder
transit3.0.23.2.3transitTo updatetransitTRANSITTransposon predictionDNA, Sequencing, Mobile genetic elementsTRANSITA tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.To updatehttps://github.com/mad-lab/transit/Genome annotationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/
transtermhp2.09transtermhpTo updateFinds rho-independent transcription terminators in bacterial genomesTo updateSequence Analysistranstermhpiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp
trinity2.15.12.15.1trinityUp-to-datetrinityTrinityTranscriptome assemblyTranscriptomics, Gene expression, Gene transcriptsTrinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseqTrinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.Up-to-datehttps://github.com/trinityrnaseq/trinityrnaseqTranscriptomics, RNAiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity
trinotate3.2.24.0.2trinotateTo updatetrinotateTrinotateGene functional annotationGene expression, TranscriptomicsTrinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.To updatehttps://trinotate.github.io/Transcriptomics, RNAtrinotateiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate
trycycler0.5.40.5.4trycyclerUp-to-dateTrycycler toolkit wrappersUp-to-datehttps://github.com/rrwick/TrycyclerAssemblytrycycleriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler
tsebra1.1.21.1.2tsebraUp-to-dateThis tool has been developed to combine BRAKER predictions.Up-to-datehttps://github.com/Gaius-Augustus/TSEBRAGenome annotationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra
tsne0.0.20.13r-rtsneTo updateT-Distributed Stochastic Neighbor Embedding using a Barnes-Hut ImplementationTo updatehttps://cran.r-project.org/web/packages/Rtsne/Text Manipulationtsneiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne
tximport1.22.01.28.0bioconductor-tximportTo updatetximporttximportPathway or network analysis, Formatting, RNA-Seq analysisTranscriptomics, Gene transcripts, WorkflowsWrapper for the Bioconductor package tximportAn R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.To updatehttp://bioconductor.org/packages/tximport/Transcriptomicstximportiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport
ucsc_blat377445ucsc-blatTo updateblatBLATSequence alignmentSequence analysisStandalone blat sequence search command line toolFast, accurate spliced alignment of DNA sequences.To updatehttp://genome.ucsc.edu/goldenPath/help/blatSpec.htmlSequence Analysisucsc_blatyating-l
fasplit377377ucsc-fasplitUp-to-dateUCSC_Genome_Browser_UtilitiesUCSC Genome Browser UtilitiesSequence analysisfaSplit is a tool to split a single FASTA file into several filesUtilities for handling sequences and assemblies from the UCSC Genome Browser project.Up-to-datehttp://hgdownload.cse.ucsc.edu/admin/exe/Fasta Manipulationucsc_fasplitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit
fatovcf448448ucsc-fatovcfUp-to-dateUCSC_Genome_Browser_UtilitiesUCSC Genome Browser UtilitiesSequence analysisConvert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffsUtilities for handling sequences and assemblies from the UCSC Genome Browser project.Up-to-datehttp://hgdownload.cse.ucsc.edu/admin/exe/Convert Formatsucsc_fatovcfiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf
twobittofa377447ucsc-twobittofaTo updateUCSC_Genome_Browser_UtilitiesUCSC Genome Browser UtilitiesSequence analysistwoBitToFa is a tool to convert all or part of .2bit file to FASTAUtilities for handling sequences and assemblies from the UCSC Genome Browser project.To updatehttps://genome.ucsc.edu/goldenpath/help/twoBit.htmlConvert Formatsucsc_twobittofaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa
umi_tools1.1.21.1.4umi_toolsTo updateumi-toolsUMI-toolsSequencing quality controlNGS, Sequence sites, features and motifs, Quality affairsUMI-tools extract - Extract UMIs from fastqTools for handling Unique Molecular Identifiers in NGS data sets.To updatehttps://github.com/CGATOxford/UMI-toolsSequence Analysis, Transcriptomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools
unicycler0.5.00.5.0unicyclerUp-to-dateunicyclerUnicyclerGenome assembly, AggregationMicrobiology, Genomics, Sequencing, Sequence assemblyUnicycler is a hybrid assembly pipeline for bacterial genomes.A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.Up-to-datehttps://github.com/rrwick/UnicyclerAssemblyunicycleriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler
usher0.2.10.6.2usherTo updateUShER toolkit wrappersTo updatehttps://github.com/yatisht/usherPhylogeneticsusheriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/usher
valet1.0valetTo updateA pipeline for detecting mis-assemblies in metagenomic assemblies.To updatehttps://github.com/marbl/VALETMetagenomicsvaletiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/valet
vapor1.0.21.0.2vaporUp-to-datevaporVAPORData retrieval, De-novo assembly, Read mappingWhole genome sequencing, Mapping, Sequence assemblyClassify Influenza samples from raw short read sequence dataVAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.Up-to-datehttps://github.com/connor-lab/vaporSequence Analysisvaporiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor
vardict1.8.3pythonTo updateVarDict - calls SNVs and indels for tumour-normal pairsTo updatehttps://github.com/AstraZeneca-NGS/VarDictJavaVariant Analysisvardict_javaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict
variant_analyzer2.0.0matplotlibTo updateCollection of tools for analyzing variants in duplex consensus sequencing (DCS) dataTo updateVariant Analysisvariant_analyzeriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer
varscan2.4.32.4.6varscanTo updateVarScan is a variant caller for high-throughput sequencing dataTo updatehttps://dkoboldt.github.io/varscan/Variant Analysisvarscaniuchttps://github.com/galaxyproject/iuc/tree/master/tools/varscan
vcf2maf1.6.211.6.21vcf2mafUp-to-datevcf2maf: Convert VCF into MAFUp-to-dateConvert Formatsvcf2mafiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf
vcfanno0.3.30.3.3vcfannoUp-to-datevcfannovcfannoSNP annotationGenetic variation, Data submission, annotation and curationAnnotate VCF filesFast, flexible annotation of genetic variants.Up-to-datehttps://github.com/brentp/vcfannoVariant Analysisvcfannoiuchttps://github.com/galaxyproject/tools-iuc/vcfanno/
vegan2.4-32.3_4r-veganTo updateTo updatehttps://cran.r-project.org/package=veganMetagenomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/
velocyto0.17.170.17.17velocyto.pyUp-to-dateVelocyto is a library for the analysis of RNA velocity.Up-to-datehttp://velocyto.org/Transcriptomicsvelocytoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto
velvet1.2.10velvetTo updatevelvetVelvetFormatting, De-novo assemblySequence assemblyde novo genomic assembler specially designed for short read sequencing technologiesA de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.To updatehttps://www.ebi.ac.uk/~zerbino/velvet/Assemblyvelvetdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet
velvet_optimiser2.2.6+galaxy21.2.10velvetTo updatevelvetoptimiserVelvetOptimiserOptimisation and refinement, Sequence assemblyGenomics, Sequence assemblyAutomatically optimize Velvet assembliesThis tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.To updateAssemblyvelvetoptimisersimon-gladmanhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser
verkko1.3.11.4.1verkkoTo updateTelomere-to-telomere assembly pipelineTo updatehttps://github.com/marbl/verkkoAssemblyverkkoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko
vg1.23.01.52.0vgTo updateVariation graph data structures, interchange formats, alignment, genotyping, and variant calling methodsTo updatehttps://github.com/vgteam/vgSequence Analysis, Variant Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vg
virhunter1.0.0numpyTo updatevirhunterVirHunterSequence classificationVirologyDeep Learning method for novel virus detection in sequencing dataVirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).To updatehttps://github.com/cbib/virhunterMachine Learningvirhunteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter
volcanoplot0.0.52.2.1r-ggplot2To updateTool to create a Volcano PlotTo updateVisualization, Transcriptomics, Statisticsvolcanoplotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot
vsearch2.8.32.24.0vsearchTo updatevsearchVSEARCHDNA mapping, Chimera detectionMetagenomics, Sequence analysisVSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.To updatehttps://github.com/torognes/vsearchSequence Analysisvsearchiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch
vsnp3.0.60.22.0pysamTo updateThe vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.To updatehttps://github.com/USDA-VS/vSNPSequence Analysisvsnpiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp
weather_app0.1.2curlTo updateprovides simple weather in text formatTo updatehttp://wttr.in/Visualization, Web Servicessimpleweatheriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app
weblogo33.5.03.7.9weblogoTo updateweblogoWebLogoSequence cluster visualisation, Sequence visualisation, Sequence motif recognitionNucleic acid sites, features and motifs, Sequence analysisSequence Logo generator for fastaWeb-based application designed to make generate sequence logos.To updateGraphicsweblogo3devteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3
winnowmap2.032.03winnowmapUp-to-dateA long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences.Up-to-datehttps://github.com/marbl/WinnowmapNext Gen Mapperswinnowmapiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap
xpath1.47perl-xml-xpathTo updateXPath XML querying toolTo updatehttp://search.cpan.org/dist/XML-XPath/Text Manipulationxpathiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath
yahs1.2a.21.2a.2yahsUp-to-dateYet Another Hi-C scaffolding toolUp-to-datehttps://github.com/c-zhou/yahsAssemblyyahsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs
zerone1.01.0zeroneUp-to-dateChIP-seq discretization and quality controlUp-to-datehttps://github.com/nanakiksc/zeroneChIP-seqzeroneiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone
bamtools2.5.22.5.2bamtoolsUp-to-dateOperate on and transform BAM datasets in various ways using bamtoolsUp-to-datehttps://github.com/pezmaster31/bamtoolsSequence Analysis, SAMbamtoolsdevteamhttps://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools
bamtools_filter2.5.22.5.2bamtoolsUp-to-dateFilter BAM datasets on various attributes using bamtools filterUp-to-datehttps://github.com/pezmaster31/bamtoolsSequence Analysis, SAMbamtools_filterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter
bamtools_split2.5.22.5.2bamtoolsUp-to-dateUp-to-datehttps://github.com/pezmaster31/bamtoolsSequence Analysis, SAMiuchttps://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split
biotradis1.4.51.4.5biotradisUp-to-dateBio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.Up-to-datehttps://www.sanger.ac.uk/science/tools/bio-tradisGenome annotationbiotradisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis
cuffcompare2.2.12.2.1cufflinksUp-to-dateGalaxy wrappers for the Cuffcompare tool.Up-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscuffcomparedevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare
cuffdiff2.2.12.2.1cufflinksUp-to-dateGalaxy wrappers for the Cuffdiff tool.Up-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscuffdiffdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff
cufflinks2.2.12.2.1cufflinksUp-to-dateGalaxy wrappers for the Cufflinks tool.Up-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscufflinksdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks
cuffmerge2.2.12.2.1cufflinksUp-to-dateGalaxy wrappers for the Cuffmerge tool.Up-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscuffmergedevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge
cuffnorm2.2.12.2.1cufflinksUp-to-dateThe Cuffnorm toolUp-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscuffnormdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm
cuffquant2.2.12.2.1cufflinksUp-to-dateThe Cuffquant toolUp-to-datehttp://cole-trapnell-lab.github.io/cufflinks/Transcriptomicscuffquantdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant
fasta_clipping_histogram0.0.140.0.14fastx_toolkitUp-to-dateLength Distribution chartUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulation, Graphics, Statisticsfasta_clipping_histogramdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram
fasta_formatter0.0.140.0.14fastx_toolkitUp-to-dateFASTA Width formatterUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulationfasta_formatterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter
fasta_nucleotide_changer0.0.140.0.14fastx_toolkitUp-to-dateRNA/DNA converter.Up-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulationfasta_nucleotide_changerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer
fastq_quality_boxplot0.0.140.0.14fastx_toolkitUp-to-dateDraw quality score boxplotUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fastq Manipulation, Graphics, Statisticsfastq_quality_boxplotdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot
fastq_quality_converter0.0.140.0.14fastx_toolkitUp-to-dateQuality format converter (ASCII-Numeric)Up-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fastq Manipulationfastq_quality_converterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter
fastq_quality_filter0.0.140.0.14fastx_toolkitUp-to-dateFilter by qualityUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fastq Manipulationfastq_quality_filterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter
fastq_to_fasta0.0.140.0.14fastx_toolkitUp-to-dateFASTQ to FASTA converterUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulation, Convert Formatsfastq_to_fastadevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta
fastx_artifacts_filter0.0.140.0.14fastx_toolkitUp-to-dateRemove sequencing artifactsUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulation, Fastq Manipulationfastx_artifacts_filterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter
fastx_barcode_splitter0.0.140.0.14fastx_toolkitUp-to-dateBarcode SplitterUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulation, Fastq Manipulationfastx_barcode_splitterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter
fastx_clipper0.0.140.0.14fastx_toolkitUp-to-dateClip adapter sequencesUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulation, Fastq Manipulationfastx_clipperdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper
fastx_collapser0.0.140.0.14fastx_toolkitUp-to-dateCollapse sequencesUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulationfastx_collapserdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser
fastx_nucleotides_distribution0.0.140.0.14fastx_toolkitUp-to-dateDraw nucleotides distribution chartUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fastq Manipulation, Graphicsfastx_nucleotides_distributiondevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution
fastx_quality_statistics0.0.140.0.14fastx_toolkitUp-to-dateCompute quality statisticsUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fastq Manipulation, Statisticsfastx_quality_statisticsdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics
fastx_renamer0.0.140.0.14fastx_toolkitUp-to-dateRename sequencesUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulation, Fastq Manipulationfastx_renamerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer
fastx_reverse_complement0.0.140.0.14fastx_toolkitUp-to-dateReverse-ComplementUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fastq Manipulation, Fasta Manipulationfastx_reverse_complementdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement
fastx_trimmer0.0.140.0.14fastx_toolkitUp-to-dateTrim sequencesUp-to-datehttp://hannonlab.cshl.edu/fastx_toolkit/Fasta Manipulation, Fastq Manipulationfastx_trimmerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer
fastq_combiner1.1.51.1.5galaxy_sequence_utilsUp-to-dateCombine FASTA and QUAL into FASTQUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulation, Fasta Manipulationfastq_combinerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner
fastq_filter1.1.51.1.5galaxy_sequence_utilsUp-to-dateFilter FASTQ reads by quality score and lengthUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_filterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter
fastq_groomer1.1.51.1.5galaxy_sequence_utilsUp-to-dateConvert between various FASTQ quality formats.Up-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_groomerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer
fastq_manipulation1.1.51.1.5galaxy_sequence_utilsUp-to-dateManipulate FASTQ reads on various attributes.Up-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_manipulationdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation
fastq_masker_by_quality1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ Masker by quality scoreUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_masker_by_qualitydevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality
fastq_paired_end_deinterlacer1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ de-interlacer on paired end reads.Up-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_paired_end_deinterlacerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer
fastq_paired_end_interlacer1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ interlacer on paired end readsUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_paired_end_interlacerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer
fastq_paired_end_joiner1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ joiner on paired end readsUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_paired_end_joinerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner
fastq_paired_end_splitter1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ splitter on joined paired end readsUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_paired_end_splitterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter
fastq_stats1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ Summary Statistics by columnUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_statsdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats
fastq_to_tabular1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ to Tabular converterUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_to_tabulardevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular
fastq_trimmer1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ Trimmer by qualityUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastq_trimmerdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer
fastqtofasta1.1.51.1.5galaxy_sequence_utilsUp-to-dateFASTQ to FASTA converterUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationfastqtofastadevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta
tabular_to_fastq1.1.51.1.5galaxy_sequence_utilsUp-to-dateTabular to FASTQ converterUp-to-datehttps://github.com/galaxyproject/sequence_utilsFastq Manipulationtabular_to_fastqdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq
kraken1.1.1krakenTo updateKraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.To updatehttp://ccb.jhu.edu/software/kraken/Metagenomicskrakendevteamhttps://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/
kraken22.1.12.1.3kraken2To updateKraken2 for taxonomic designation.To updatehttp://ccb.jhu.edu/software/kraken/Metagenomicskraken2iuchttps://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/
samtools1.15.11.18samtoolsTo updateTo updateSAMiuc
snpeff1.70biopythonTo updateSnpEff is a genetic variant annotation and effect prediction toolboxTo updatehttp://snpeff.sourceforge.net/Genome-Wide Association Study, Variant Analysissnpeffiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff
snpsift5.2snpsiftTo updatesnpEff SnpSift tools from Pablo CingolaniTo updatehttp://snpeff.sourceforge.net/SnpSift.htmlVariant Analysissnpsiftiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift
snpsift_dbnsfp5.2snpsiftTo updatesnpEff SnpSift dbnsfp tool from Pablo CingolaniTo updatehttp://snpeff.sourceforge.net/SnpSift.html#dbNSFPVariant Analysissnpsift_dbnsfpiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp
snpsift_genesets5.2snpsiftTo updateAnnotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, ReactomeTo updatehttp://snpeff.sourceforge.net/SnpSift.html#geneSetsVariant Analysissnpsift_genesetsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/
vcf2tsv1.0.9vcflibTo updateConverts VCF files into tab-delimited formatTo updatehttps://github.com/ekg/vcflibVariant Analysis, Convert Formatsvcf2tsvdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv
vcfaddinfo1.0.9vcflibTo updateAdds info fields from the second dataset which are not present in the first dataset.To updatehttps://github.com/ekg/vcflibVariant Analysisvcfaddinfodevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo
vcfallelicprimitives1.0.9vcflibTo updateSplits alleleic primitives (gaps or mismatches) into multiple VCF linesTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfallelicprimitivesdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives
vcfannotate1.0.9vcflibTo updateIntersect VCF records with BED annotationsTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfannotatedevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate
vcfannotategenotypes1.0.9vcflibTo updateAnnotate genotypes in a VCF dataset using genotypes from another VCF dataset.To updatehttps://github.com/ekg/vcflibVariant Analysisvcfannotategenotypesdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes
vcfbedintersect1.0.9vcflibTo updateIntersect VCF and BED datasetsTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfbedintersectdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect
vcfbreakcreatemulti1.0.9vcflibTo updateBreak multiple alleles into multiple records, or combine overallpoing alleles into a single recordTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfbreakcreatemultidevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti
vcfcheck1.0.9vcflibTo updateVerify that the reference allele matches the reference genomeTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfcheckdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck
vcfcombine1.0.9vcflibTo updateCombine multiple VCF datasetsTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfcombinedevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine
vcfcommonsamples1.0.9vcflibTo updateOutput records belonging to samples commong between two datasets.To updatehttps://github.com/ekg/vcflibVariant Analysisvcfcommonsamplesdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples
vcfdistance1.0.9vcflibTo updateCalculate distance to the nearest variant.To updatehttps://github.com/ekg/vcflibVariant Analysisvcfdistancedevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance
vcffilter1.0.9vcflibTo updateTool for filtering VCF filesTo updatehttps://github.com/ekg/vcflibVariant Analysisvcffilterdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter
vcffixup1.0.9vcflibTo updateCount the allele frequencies across alleles present in each record in the VCF file.To updatehttps://github.com/ekg/vcflibVariant Analysisvcffixupdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup
vcfflatten1.0.9vcflibTo updateRemoves multi-allelic sites by picking the most common alternateTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfflattendevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten
vcfgeno2haplo1.0.9vcflibTo updateConvert genotype-based phased alleles into haplotype allelesTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfgeno2haplodevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo
vcfgenotypes1.0.9vcflibTo updateConvert numerical representation of genotypes to allelic.To updatehttps://github.com/ekg/vcflibVariant Analysisvcfgenotypesdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes
vcfhethom1.0.9vcflibTo updateCount the number of heterozygotes and alleles, compute het/hom ratio.To updatehttps://github.com/ekg/vcflibVariant Analysisvcfhethomdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom
vcfleftalign1.0.9vcflibTo updateLeft-align indels and complex variants in VCF datasetTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfleftaligndevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign
vcfprimers1.0.9vcflibTo updateExtract flanking sequences for each VCF recordTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfprimersdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers
vcfrandomsample1.0.9vcflibTo updateRandomly sample sites from VCF datasetTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfrandomsampledevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample
vcfselectsamples1.0.9vcflibTo updateSelect samples from a VCF fileTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfselectsamplesdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples
vcfsort1.0.9vcflibTo updateSort VCF dataset by coordinateTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfsortdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort
vcfvcfintersect1.0.9vcflibTo updateIntersect two VCF datasetsTo updatehttps://github.com/ekg/vcflibVariant Analysisvcfvcfintersectdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect
ThermoRawFileParser1.3.41.4.3thermorawfileparserTo updateThermo RAW file converterTo updatehttps://github.com/compomics/ThermoRawFileParserProteomicsthermo_raw_file_convertergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser
appendfdr0.2.0To updateTo updateappendfdrgalaxyp
bed_to_protein_map0.2.0pythonTo updateConverts a BED file to a tabular list of exon locationsTo updateProteomicsbed_to_protein_mapgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map
blast_plus_remote_blastp2.6.02.14.1blastTo updateNCBI BLAST+ with -remote optionTo updatehttps://blast.ncbi.nlm.nih.gov/Sequence Analysisblast_plus_remote_blastpgalaxyphttps://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus
bumbershoot3.0.211423_0_21142_0e4f4a4bumbershootTo updateTo updatehttp://proteowizard.sourceforge.net/Proteomicsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
calisp3.0.133.0.13calispUp-to-dateCalgary approach to isotopes in proteomicsUp-to-datehttps://github.com/kinestetika/Calisp/Proteomicscalispgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tools/calisp
cardinal2.10.03.2.1bioconductor-cardinalTo updateStatistical and computational tools for analyzing mass spectrometry imaging datasetsTo updatehttp://cardinalmsi.orgProteomics, Metabolomicsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal
dbbuilder0.3.4wgetTo updateProtein Database DownloaderTo updatehttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilderProteomicsdbbuildergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder
decoyfastaTo updateGalaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.To updateProteomicsdecoyfastagalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta
dia_umpire2.1.32.1.6dia_umpireTo updateDIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomicsTo updatehttp://diaumpire.sourceforge.net/Proteomicsdia_umpiregalaxyphttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire
dialignr1.2.02.8.0bioconductor-dialignrTo updateDIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.To updatehttps://github.com/shubham1637/DIAlignRProteomicsdialignrgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr
diann1.8.1To updateDiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.To updatehttps://github.com/vdemichev/DiaNNProteomicsdianngalaxyphttps://github.com/vdemichev/DiaNN
diapysef0.3.5.01.0.10diapysefTo updatediapysef is a convenience package for working with DIA-PASEF dataTo updatehttps://pypi.org/project/diapysef/Proteomicsdiapysefgalaxyphttps://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef
diffacto1.0.61.0.6diffactoUp-to-dateDiffacto comparative protein abundance estimationUp-to-datehttps://github.com/statisticalbiotechnology/diffactoProteomicsdiffactogalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto
digestdb0.1.0trans_proteomic_pipelineTo updateTo updatedigestdbgalaxyp
directag_and_tagreconTo updateTo updatedirectag_and_tagrecongalaxyp
data_manager_eggnog_mapperTo updatedownloads eggnog data for eggnog-mapperTo updateProteomicsdata_manager_eggnog_mappergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager
data_manager_eggnog_mapper_abspathTo updatedownload eggnog data for eggnog-mapperTo updateProteomicsdata_manager_eggnog_mapper_abspathgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath
eggnog_mapper2.1.82.1.12eggnog-mapperTo updateeggnog-mapper-v2eggNOG-mapper v2Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrievalMetagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysiseggnog-mapper fast functional annotation of novel sequencesEggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.To updateProteomicseggnog_mappergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper
encyclopedia1.12.342.12.30encyclopediaTo updateMass Spec Data-Independent Acquisition (DIA) MS/MS analysisTo updatehttps://bitbucket.org/searleb/encyclopedia/wiki/HomeProteomicsencyclopediagalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia
fasta_merge_files_and_filter_unique_sequences1.2.0pythonTo updateConcatenate FASTA database files togetherTo updatehttps://github.com/galaxyproteomics/tools-galaxyp/Fasta Manipulationfasta_merge_files_and_filter_unique_sequencesgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences
fastg2protlib1.0.2To updateGenerate FASTA from FASTGTo updatehttps://github.com/galaxyproteomics/fastg2protlib.gitProteomicsfastg2protlibgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib
feature_alignment0.11.00.11.0msproteomicstoolsUp-to-dateTRIC integrates information from all available runs via a graph-based alignment strategyUp-to-dateProteomicsfeature_alignmentgalaxyphttps://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md
filter_by_fasta_ids2.3pythonTo updateFilter FASTA on the headers and/or the sequencesTo updateFasta Manipulation, Proteomicsfilter_by_fasta_idsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids
flashlfq1.0.3.11.2.5flashlfqTo updateFlashLFQ mass-spectrometry proteomics label-free quantificationTo updatehttps://github.com/smith-chem-wisc/FlashLFQProteomicsflashlfqgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq
gffcompare_to_bed0.2.1pythonTo updateFilter and convert a gffCompare GTF to BEDTo updatehttps://github.com/gpertea/gffcompare/Convert Formatsgffcompare_to_bedgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed
hardklor2.30.1+galaxy12.3.2hardklorTo updateHardklörTo updateProteomicshardklorgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor
idconvert3_0_9992proteowizardTo updateConvert mass spectrometry identification files on linux or MacOSXTo updateProteomicsidconvertgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert
lfq_protein_quant1.02.26.0bioconductor-msnbaseTo updateEnable protein summarisation and quantitationTo updatehttps://github.com/compomics/LFQ_galaxy_pProteomicslfq_protein_quantgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant
ltq_iquant_cliTo updateTo updateltq_iquant_cligalaxyp
maldiquant1.22.0r-baseTo updateMALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.To updatehttp://strimmerlab.org/software/maldiquant/ProteomicsMALDIquantgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant
map_peptides_to_bed0.21.70biopythonTo updateMap peptides to a reference genome for display by a genome browserTo updateProteomicsmap_peptides_to_bedgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed
maxquant2.0.3.02.0.3.0maxquantUp-to-datewrapper for MaxQuantUp-to-datehttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquantProteomicsmaxquantgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant
meta_proteome_analyzer2.0.02.0.0mpa-portableUp-to-dateMetaProteomeAnalyzerUp-to-datehttps://github.com/compomics/meta-proteome-analyzer/Proteomicsmeta_proteome_analyzergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer
metagene_annotator1.0.01.0metagene_annotatorTo updateMetaGeneAnnotator gene-finding program for prokaryote and phageTo updateSequence Analysismetagene_annotatorgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator
metanovo1.9.41.9.4metanovoUp-to-dateProduce targeted databases for mass spectrometry analysis.Up-to-datehttps://github.com/uct-cbio/proteomics-pipelinesProteomicsmetanovogalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo
metaquantome2.0.22.0.2metaquantomeUp-to-datequantitative analysis of microbiome taxonomy and functionUp-to-datehttps://github.com/galaxyproteomics/metaquantome/Proteomicsmetaquantomegalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome
mgf_formatter1.0.01.0.0mgf-formatterUp-to-dateUp-to-datemgf_formattergalaxyp
moFF2.0.32.0.3moffUp-to-datemoFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.Up-to-datehttps://github.com/compomics/moFFProteomicsproteomics_moffgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF
morpheus2.255.0287morpheusTo updateMorpheus MS Search ApplicationTo updateProteomicsmorpheusgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus
mqppep0.1.191.62.1bioconductor-preprocesscoreTo updateMaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVATo updatehttps://github.com/galaxyproteomics/tools-galaxyp/Proteomicsmqppepgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep
msconvert3.0.20287To updatemsconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker containerTo updateProteomicsmsconvertgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert
msgfplus0.52023.01.1202msgf_plusTo updateMSGF+To updateProteomicsmsgfplusgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus
msms_extractor1.0.03_0_9992proteowizardTo updateExtract MS/MS scans from the mzML file(s) based on PSM report.To updateProteomicsmsms_extractorgalaxyp
msstats4.0.04.8.3bioconductor-msstatsTo updateMSstats tool for analyzing mass spectrometry proteomic datasetsTo updatehttps://github.com/MeenaChoi/MSstatsProteomicsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats
msstatstmt2.0.02.8.0bioconductor-msstatstmtTo updateMSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labelingTo updatehttp://msstats.org/msstatstmt/Proteomicsmsstatstmtgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt
mt2mq1.1.0r-tidyverseTo updateTool to prepare metatranscriptomic outputs from ASaiM for MetaquantomeTo updateProteomicsmt2mqgalaxyp
mz_to_sqlite2.1.1+galaxy02.1.1mztosqliteTo updateCreates a SQLite database for proteomics dataTo updateProteomicsmz_to_sqlitegalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite
openms2.83.1.0openmsTo updateOpenMS Suite for LC/MS data management and analysesTo updatehttps://www.openms.de/Proteomicsopenmsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms
pathwaymatcher1.9.1pathwaymatcherTo updateReactome Pathway MatcherTo updatehttps://github.com/LuisFranciscoHS/PathwayMatcherProteomicsreactome_pathwaymatchergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher
pep_pointer0.1.3+galaxy1pythonTo updatePepPointer categorizes peptides by their genomic coordinates.To updateGenomic Interval Operations, Proteomicspep_pointergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer
pepquery1.6.22.0.2pepqueryTo updateA peptide-centric MS search engine for novel peptide identification and validation.To updatehttps://pepquery.orgProteomicspepquerygalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery
pepquery22.0.22.0.2pepqueryUp-to-datePepQuery2 peptide-centric MS search for peptide identification and validationUp-to-datehttps://pepquery.orgProteomicspepquery2galaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2
peptide_genomic_coordinate1.0.0pythonTo updateGets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite filesTo updateProteomicspeptide_genomic_coordinategalaxyp
peptideshaker4.3.1searchguiTo updatePeptideShaker and SearchGUITo updatehttp://compomics.github.ioProteomicspeptideshakergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker
pepxml_to_xlsTo updateConvert PepXML to TabularTo updateProteomicspepxml_to_xlsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls
percolator3.53.5percolatorUp-to-datePercolatorUp-to-dateProteomicspercolatorgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tools/percolator
pi_db_tools1.3pythonTo updateHiRIEF toolsTo updateProteomicshirieftoolsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools
pmd_fdr1.4.0r-baseTo updateCalculate Precursor Mass Discrepancy (PMD) for MS/MSTo updatehttps://github.com/slhubler/PMD-FDR-for-Galaxy-PProteomicspmd_fdrgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr
custom_pro_db1.22.01.37.1bioconductor-rgalaxyTo updateCustomProDBTo updatehttps://bioconductor.org/packages/release/bioc/html/customProDB.htmlProteomicscustom_pro_dbgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db
custom_pro_db_annotation_data_managerTo updateCustomProDB AnnotationTo updatehttps://bioconductor.org/packages/release/bioc/html/customProDB.htmlProteomicscustom_pro_db_annotation_data_managergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db
psm2sam1.3.2.1r-baseTo updatePSM to SAMTo updatehttps://bioconductor.org/packages/release/bioc/html/proBAMr.htmlProteomicspsm_to_samgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam
proteinpilot0.1To updateTo updateproteinpilotgalaxyp
retrieve_ensembl_bed0.1.0To updateRetrieve cDNA features from Ensembl REST API in BED formatTo updatehttp://rest.ensembl.org/Data Sourceretrieve_ensembl_bedgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed
translate_bed0.1.0To updateTranslate BED transcript CDS or cDNA in 3 framesTo updatehttp://rest.ensembl.org/Proteomicstranslate_bedgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed
proteomiqon_joinquantpepionswithproteins0.0.10.0.2proteomiqon-joinquantpepionswithproteinsTo updateThe tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.To updatehttps://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.htmlProteomicsproteomiqon_joinquantpepionswithproteinsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins
proteomiqon_labeledproteinquantification0.0.10.0.3proteomiqon-labeledproteinquantificationTo updateThe tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.To updatehttps://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.htmlProteomicsproteomiqon_labeledproteinquantificationgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification
proteomiqon_labelfreeproteinquantification0.0.10.0.3proteomiqon-labelfreeproteinquantificationTo updateThe tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.To updatehttps://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.htmlProteomicsproteomiqon_labelfreeproteinquantificationgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification
proteomiqon_mzmltomzlite0.0.80.0.8proteomiqon-mzmltomzliteUp-to-dateThe tool MzMLToMzLite allows to convert mzML files to mzLite files.Up-to-datehttps://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.htmlProteomicsproteomiqon_mzmltomzlitegalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite
proteomiqon_peptidedb0.0.70.0.7proteomiqon-peptidedbUp-to-dateThe tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.Up-to-datehttps://csbiology.github.io/ProteomIQon/tools/PeptideDB.htmlProteomicsproteomiqon_peptidedbgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb
proteomiqon_peptidespectrummatching0.0.70.0.7proteomiqon-peptidespectrummatchingUp-to-dateGiven raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.Up-to-datehttps://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.htmlProteomicsproteomiqon_peptidespectrummatchinggalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching
proteomiqon_proteininference0.0.70.0.7proteomiqon-proteininferenceUp-to-dateMS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.Up-to-datehttps://csbiology.github.io/ProteomIQon/tools/ProteinInference.htmlProteomicsproteomiqon_proteininferencegalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference
proteomiqon_psmbasedquantification0.0.80.0.9proteomiqon-psmbasedquantificationTo updateThe PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.To updatehttps://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.htmlProteomicsproteomiqon_psmbasedquantificationgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification
proteomiqon_psmstatistics0.0.80.0.8proteomiqon-psmstatisticsUp-to-dateThe PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.Up-to-datehttps://csbiology.github.io/ProteomIQon/tools/PSMStatistics.htmlProteomicsproteomiqon_psmstatisticsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics
proteore_venn_diagram2021.06.08pythonTo updateProteoRE JVenn DiagramTo updateProteomicsproteore_venn_diagramgalaxyp
protxml_to_xls0.1.0trans_proteomic_pipelineTo updateTo updateprotxml_to_xlsgalaxyp
psm_eval0.1.0binaries_for_psm_evalTo updateTo updatepsm_evalgalaxyp
psm_validation1.0.3To updateValidate PSM from Ion FragmentationTo updatehttps://github.com/galaxyproteomics/psm_fragments.gitProteomicspsm_validationgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation
pyprophet2.1.42.2.5pyprophetTo updateSemi-supervised learning and scoring of OpenSWATH results.To updatehttps://github.com/PyProphet/pyprophetProteomicsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet
pyteomics4.4.14.6.2pyteomicsTo updatepyteomicsPyteomicsProtein identificationProteomics, Proteomics experimentTools using the pyteomics libraryFramework for proteomics data analysis, supporting mzML, MGF, pepXML and more.To updatehttps://pyteomics.readthedocs.io/en/latest/Proteomics, Metabolomicspyteomicsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics
quantp1.1.21.11.6r-data.tableTo updateCorrelation between protein and transcript abundanceTo updateProteomicsquantpgalaxyp
quantwiz_iq2.02.0quantwiz-iqUp-to-dateIsobaric Quantitation using QuantWiz-IQUp-to-datehttps://sourceforge.net/projects/quantwiz/Proteomicsquantwiz_iqgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq
qupath_roi_splitter0.1.0+galaxy1geojsonTo updateSplit ROI coordinates of QuPath TMA annotation by cell typeTo updatehttps://github.com/npinter/ROIsplitterImagingqupath_roi_splittergalaxyphhttps://github.com/npinter/ROIsplitter
rawtools2.0.4rawtoolsTo updateRaw ToolsTo updatehttps://github.com/kevinkovalchik/RawToolsProteomicsrawtoolsgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools
regex_find_replace1.0.3pythonTo updateUse python regular expressions to find and replace textTo updateText Manipulationregex_find_replacegalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace
scaffold0.1.0scaffoldTo updateTo updatescaffoldgalaxyp
sixgill0.2.40.2.4sixgillUp-to-dateSix-frame Genome-Inferred Libraries for LC-MS/MSUp-to-dateProteomics, MetaProteomicssixgillgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill
spectrast2spectrast_irt0.1.00.11.0msproteomicstoolsTo updateFilter from spectraST files to swath input filesTo updateProteomicsspectrast2spectrast_irtgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt
spectrast2tsv0.1.00.11.0msproteomicstoolsTo updateFilter from spectraST files to swath input filesTo updateProteomicsspectrast2tsvgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv
translate_bed_sequences0.2.01.70biopythonTo updatePerform 3 frame translation of BED file augmented with a sequence columnTo updateProteomicstranslate_bed_sequencesgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences
unipept4.5.1pythonTo updateUnipept retrieves metaproteomics informationTo updatehttps://github.com/galaxyproteomics/tools-galaxypProteomicsunipeptgalaxyphttps://unipept.ugent.be/apidocs
uniprotxml_downloader2.4.0requestsTo updateDownload UniProt proteome in XML or fasta formatTo updateProteomicsuniprotxml_downloadergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader
validate_fasta_database0.1.51.0validate-fasta-databaseTo updateruns Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.To updateFasta Manipulation, Proteomicsvalidate_fasta_databasegalaxyp
bio3d2.4_12.3_3r-bio3dTo updateBio3d is a program that can be used to analyse molecular dynamics trajectories.To updatehttp://thegrantlab.org/bio3d/index.phpComputational chemistrybio3dchemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d
biomoldyn1.5.2scipyTo updateTools for MD analysisTo updatehttps://github.com/moldyn/Molecular Dynamics, Computational chemistrybiomoldynchemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/
ambertools21.10ambertoolsTo updateAmbertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.To updatehttp://ambermd.org/AmberTools.phpMolecular Dynamics, Computational chemistryambertoolschemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/
packmol18.169.1packmolTo updatePACKMOL is a package for creating starting structures for Molecular Dynamics simulationsTo updatehttp://m3g.iqm.unicamp.br/packmol/home.shtmlMolecular Dynamics, Computational chemistrypackmolchemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem
topologyeditors0pythonTo updateSet of python scripts and associated tool files that can be used to modify topology files.To updatehttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditorsMolecular Dynamics, Computational chemistrytopologyeditorschemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors
free_energyTo updateFree energy tools of BRIDGE.To updateMolecular Dynamics, Computational chemistryfreeenergychemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy
gromacs20222021.3gromacsTo updateGROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids.To updatehttps://github.com/gromacsMolecular Dynamics, Computational chemistrygromacschemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs
mdanalysis1.0.0mdanalysisTo updateMDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulationsTo updatehttps://github.com/MDAnalysis/mdanalysisComputational chemistrymdanalysischemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/
mdfileconverter1.9.7mdtrajTo updateA tool for interconverting between different MD structure and trajectory file formats.To updateMolecular Dynamics, Computational chemistrymd_converterchemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter
mdslicer1.9.7mdtrajTo updateA tool for slicing trajectory files using MDTraj.To updateMolecular Dynamics, Computational chemistrymd_converterchemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer
mdtraj1.9.7mdtrajTo updateMDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectoriesTo updatehttps://github.com/mdtraj/mdtrajComputational chemistrymdtrajchemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/
openmm1.8.1pdbfixerTo updateOpenMM is a toolkit for molecular simulation using high performance GPU code.To updatehttps://github.com/openmmMolecular Dynamics, Computational chemistryopenmmchemteamhttps://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm
vmdTo updatevmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulationsTo updatehttps://www.ks.uiuc.edu/Research/vmd/Computational chemistryvmdchemteamhttps://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd
artbio_bam_cleaning1.10+galaxy01.18samtoolsTo updatefilter bam files before somatic-varscan or lumpy-smoove analysisTo updatehttp://artbio.frSAM, Variant Analysisartbio_bam_cleaningartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning
bamparse4.1.10.22.0pysamTo updateGenerates hit count lists from bam alignments.To updatehttp://artbio.frRNA, Transcriptomicsbamparseartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse
bigwig_to_bedgraph377+galaxy1448ucsc-bigwigtobedgraphTo updateConverts a bigWig file to bedGraph formatTo updatehttp://artbio.frConvert Formatsbigwig_to_bedgraphartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph
bigwig_to_wig3+galaxy0377ucsc-bigwiginfoTo updateConverts a bigWig file to Wiggle (WIG) formatTo updatehttps://artbio.frConvert Formatsbigwig_to_wigartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig
blast_to_scaffold1.1.0pythonTo updateGenerate DNA scaffold from blastn or tblastx alignments of ContigsTo updatehttp://artbio.frRNA, Sequence Analysis, Assemblyblast_to_scaffoldartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold
blast_unmatched1.0.1pythonTo updateExtract unmatched query sequences from blastTo updatehttp://artbio.frFasta Manipulationblast_unmatchedartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched
blastparser_and_hits2.7.1pythonTo updateParse blast outputs and compile hitsTo updatehttp://artbio.frAssembly, RNAblastparser_and_hitsartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits
blastx_to_scaffold1.1.1pythonTo updateGenerate DNA scaffold from blastx alignment of ContigsTo updatehttp://artbio.frRNA, Sequence Analysis, Assemblyblastx_to_scaffoldartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold
cap32.0.110.2011cap3To updatecap3 wrapperTo updatehttp://artbio.frAssemblycap3artbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/cap3
cherry_pick_fasta4.1pythonTo updatePick fasta sequence with specific header contentTo updatehttp://artbio.frFasta Manipulationcherry_pick_fastaartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta
concat_multi_datasets1.4.2To updateConcatenate multiple datasets tail-to-head, including collection datasets.To updatehttp://artbio.frText Manipulationconcatenate_multiple_datasetsartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets
cpm_tpm_rpk0.5.21.3.2r-optparseTo updateGenerate CPM,TPM or RPK from raw countsTo updatehttp://artbio.frTranscriptomicscpm_tpm_rpkartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk
deseq2_normalization1.40.2+galaxy01.40.2bioconductor-deseq2To updateNormalizes gene hitlistsTo updatehttp://artbio.frRNA, Transcriptomics, Sequence Analysis, Statisticsdeseq2_normalizationartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization
embl2fa0.2To updateConverts EMBL flat format to fasta formatTo updatehttp://artbio.frText Manipulationembl2faartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa
fetch_fasta_from_ncbi3.1.01.12urllib3To updateFetch fasta sequences from NCBI using eutils wrappersTo updatehttp://artbio.frFasta Manipulation, Data Sourcefetch_fasta_from_ncbiartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi
fisher_test2.32.0+galaxy02.32.0bioconductor-qvalueTo updateFisher's exact test on two-column hit lists.To updatehttp://artbio.frRNA, Statisticsfishertestartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test
gatk44.1.7.04.4.0.0gatk4To updateFind somatic variationsTo updatehttp://artbio.frVariant Analysisgatk4artbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4
get_reference_fasta0.3.2To updateObtain reference genome sequence.To updatehttp://artbio.frData Source, Fasta Manipulationget_reference_fastaartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta
gsc_center_scale4.3.1+galaxy01.3.2r-optparseTo updateCenter or scale (standardize) dataTo updatehttp://artbio.frStatisticsgsc_center_scaleartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale
gsc_filter_cells4.3.1+galaxy01.3.2r-optparseTo updateFilter single cell RNAseq data on libray depth and number of detected genesTo updatehttp://artbio.frTranscriptomicsgsc_filter_cellsartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells
gsc_filter_genes4.3.1+galaxy01.3.2r-optparseTo updateFilter genes that are detected in less than a fraction of libraries in single cell RNAseq dataTo updatehttp://artbio.frTranscriptomicsgsc_filter_genesartbiohttps://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes
gsc_gene_expression_correlations4.3.1+galaxy01.3.2r-optparseTo updateCompute single-cell paire-wise gene expressions correlationsTo updatehttp://artbio.frTranscriptomicsgsc_gene_expression_correlationsartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations
gsc_high_dimensions_visualisation0.9.61.3.2r-optparseTo updateGenerates PCA, t-SNE and HCPC visualisationTo updatehttp://artbio.frTranscriptomics, Visualizationgsc_high_dimensions_visualisationartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization
gsc_mannwhitney_de0.9.41.3.2r-optparseTo updatePerform a mann-whitney differential testing between two sets of gene expression dataTo updatehttp://artbio.frTranscriptomicsgsc_mannwhitney_deartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de
gsc_scran_normalize0.2.11.3.2r-optparseTo updateNormalize raw counts using scranTo updatehttp://artbio.frTranscriptomicsgsc_scran_normalizeartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize
gsc_signature_score0.9.11.3.2r-optparseTo updateCompute signature scores from single cell RNAseq dataTo updatehttp://artbio.frTranscriptomicsgsc_signature_scoreartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score
guppy0.2.1To updateA wrapper for the guppy basecaller tool from Oxford Nanopore TechnologiesTo updatehttp://artbio.frNanoporeguppy_basecallerartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/guppy
high_dim_heatmap1.2.02.17.0r-gplotsTo updategplot heatmap.2 function adapted for plotting large heatmapsTo updatehttps://github.com/cran/gplotsVisualizationhigh_dim_heatmapartbiohttps://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap
justdiff0.6.0To updateUnix diffTo updatehttp://artbio.frText Manipulationjustdiffartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/justdiff
justgzip0.2To updateCompress fastq sequence filesTo updatehttp://artbio.frConvert Formatsjustgzipartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip
lumpy_smoove0.2.8+galaxy00.7.1svtyperTo updateGalaxy wrapper of the lumpy-using smoove workflowTo updatehttp://artbio.frVariant Analysislumpy_smooveartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove
lumpy_sv1.2.20.3.1lumpy-svTo updateFind structural variationsTo updatehttp://artbio.frVariant Analysislumpy_svartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv
manta1.61.18samtoolsTo updateStructural variant and indel caller for mapped sequencing dataTo updatehttp://artbio.frVariant Analysismantaartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/manta
mapping_quality_stats0.19.1+galaxy01.3.2r-optparseTo updateCollects and shows the distribution of MAPQ values in a BAM alignment fileTo updatehttp://artbio.frSequence Analysis, Statisticsmapping_quality_statsartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats
mircounts1.5.1tarTo updateGenerates miRNA count lists from read alignments to mirBase.To updatehttp://artbio.frRNA, Transcriptomicsmircountsartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts
mutational_patterns3.4.0+galaxy23.10.0bioconductor-mutationalpatternsTo updateMutational patterns and signatures in base substitution catalogsTo updatehttp://artbio.frVariant Analysismutational_patternsartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns
oases1.3.00.2.09oasesTo updateShort read assemblerTo updatehttp://artbio.frAssembly, RNAoasesartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/oases
pathifier1.0.21.3.2r-optparseTo updatepathifierTo updatehttps://Transcriptomics, Statisticspathifierartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier
pindel0.2.5b8+galaxy10.2.5b9pindelTo updatePindel detects genome-wide structural variation.To updatehttp://artbio.frVariant Analysispindelartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/pindel
probecoverage0.7.01.18samtoolsTo updatecomputes and plots read coverage of genomic regions by sequencing datasetsTo updatehttp://artbio.frSequence Analysis, Genomic Interval Operations, Graphics, Statisticsprobecoverageartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage
repenrich1.5.23.42.4bioconductor-edgerTo updateRepeat element profilingTo updatehttps://github.com/nskvir/RepEnrichTranscriptomics, Variant Analysisrepenrichartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich
rsem1.3.3rsemTo updatetranscript quantification from RNA-Seq dataTo updatehttps://github.com/deweylab/RSEMTranscriptomics, RNArsemartbiohttps://github.com/artbio/tools-artbio/tree/master/tools/rsem
sambamba0.7.1+galaxy11.0sambambaTo updatefilter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAMTo updatehttp://artbio.frSAMsambambaartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba
sashimi_plot0.1.1pythonTo updateGenerates a sashimi plot from bam files.To updatehttp://artbio.frRNA, Transcriptomics, Graphics, Visualizationsashimi_plotartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot
sequence_format_converter2.2.0pythonTo updatevarious fasta to tabular conversionsTo updatehttp://artbio.frConvert Formats, Fasta Manipulationsequence_format_converterartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter
small_rna_clusters1.3.00.22.0pysamTo updateclusters small rna reads in alignment BAM filesTo updatehttp://artbio.frRNA, SAM, Graphics, Next Gen Mapperssmall_rna_clustersartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters
small_rna_maps3.1.1numpyTo updateGenerates small read maps from alignment BAM filesTo updatehttp://artbio.frRNA, SAM, Graphics, Next Gen Mapperssmall_rna_mapsartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps
small_rna_signatures3.4.20.22.0pysamTo updateComputes the tendency of small RNAs to overlap with each other.To updatehttp://artbio.frRNAsmall_rna_signaturesartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures
snvtocnv3.0.0+galaxy13.0.0sequenza-utilsTo updateinfer copy number variations from a vcf file with SNVs using R sequenzaTo updatehttp://artbio.frVariant Analysissnvtocnvartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv
sr_bowtie2.3.01.3.1bowtieTo updatebowtie wrapper tool to align small RNA sequencing readsTo updatehttp://artbio.frRNA, Next Gen Mapperssr_bowtieartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie
sr_bowtie_dataset_annotation2.81.3.1bowtieTo updateMaps iteratively small RNA sequencing datasets to reference sequences.To updatehttp://artbio.frRNAsr_bowtie_dataset_annotationartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation
tarfast50.6.1pigzTo updateproduces a tar.gz archive of fast5 sequence filesTo updatehttp://artbio.frNanoporetarfast5artbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5
varscan_vaf0.1pythonTo updateCompute variant allele frequency in vcf files generated by varscan.To updatehttp://artbio.frVariant Analysisvarscan_vafartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf
xpore2.1+galaxy02.1xporeTo updateIdentification and quantification of differential RNA modifications from direct RNA sequencingTo updatehttps://github.com/GoekeLab/xporeNanoporexporeartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/xpore
yac_clipper2.5.1pythonTo updateClips 3' adapters for small RNA sequencing reads.To updatehttp://artbio.frRNA, Fastq Manipulationyac_clipperartbiohttps://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper
EMLassemblyline0.1.0+galaxy0r-emlassemblylineTo updateTools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versaTo updatehttps://github.com/EDIorg/EMLassemblylineEcologyemlassemblylineecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline
Ecoregionalization_workflow0.1.0+galaxy0r-baseTo updateTools to compute ecoregionalization with BRT model predictions and clustering.To updatehttps://github.com/PaulineSGN/Workflow_GalaxyEcologyecoregionalizationecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow
PAMPA0.0.2To updateTools to compute and analyse biodiversity metricsTo updateEcologypampaecologyhttps://github.com/ColineRoyaux/PAMPA-Galaxy
ab1_fastq1.20.01.36.0bioconductor-sangerseqrTo updateTool to convert ab1 files into FASTQ filesTo updateConvert Formatsab1fastqecologyhttps://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq
champ_blocs0.0.0r-baseTo updateCompute indicators for turnover boulders fieldsTo updateEcologyecologyhttps://github.com/Marie59/champ_blocs
consensus_from_alignments1.0.0r-bioseqTo updateTool to compute a consensus sequence from several aligned fasta sequencesTo updateSequence Analysisconsalignecologyhttps://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments
data_exploration0.0.0r-tanglesTo updateExplore data through multiple statistical toolsTo updateEcologyecologyhttps://github.com/Marie59/Data_explo_tools
xarray2022.3.0xarrayTo updatexarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.To updatehttp://xarray.pydata.orgEcologyecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/
gdal3.0.0To updateGeospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.To updatehttps://www.gdal.orgEcologygdalecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal
obisindicators0.0.2r-baseTo updateCompute biodiveristy indicators for marine data from obisTo updateEcologyecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators
regionalgam1.5r-mgcvTo updateTo updatehttps://github.com/RetoSchmucki/regionalGAMEcologyecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam
spocc1.2.2To updateGet species occurences dataTo updatehttps://cran.r-project.org/web/packages/spocc/index.htmlEcologyspocc_occecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc
srs_tools0.0.1r-baseTo updateCompute biodiversity indicators for remote sensing data from Sentinel 2To updateEcologyecologyhttps://github.com/Marie59/Sentinel_2A/srs_tools
stoc0.0.2To updateTools to analyse STOC data.To updateEcologystocepsecologyhttps://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc
vigiechiro0.1.1To updateTools created by the vigiechiro team to analyses and identify chiro sounds files.To updatehttps://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiroEcologyvigiechiroecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro
xmlstarlet1.6.1xmlstarletTo updateTool to convert a xml file from one metadata standard to anotherTo updateConvert Formatsxmlstarletecologyhttps://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet
c3s0.1.0pythonTo updateCopernicus Climate Change Service (C3S)To updatehttps://cds.climate.copernicus.eu/cdsapp#!/search?type=datasetClimate Analysisc3sclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s
cads0.1.0pythonTo updateCopernicus Atmosphere Data Store (ADS)To updatehttps://ads.atmosphere.copernicus.eu/#!/homeClimate Analysiscadsclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads
cdo2.0.0To updateCDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.To updatehttps://code.mpimet.mpg.de/projects/cdo/Climate Analysisclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo
cesm2.1.32.1.3cesmUp-to-dateCommunity Earth System Model (CESM)Up-to-datehttps://www.cesm.ucar.edu/Climate Analysiscesmclimatehttps://github.com/ESCOMP/CESM
climate-stripes1.0.2pythonTo updateCreate climate stripes from a tabular input fileTo updatehttps://www.climate-lab-book.ac.uk/2018/warming-stripes/Climate Analysis, Visualizationclimate_stripesclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes
eodie1.0.2eodieTo updateEarth Observation Data Information ExtractorTo updatehttps://eodie.readthedocs.io/Climate Analysiseodieclimatehttps://gitlab.com/eetun-tiimi/EODIE
essential_climate_variables0.2.0pythonTo updateGet Copernicus Essential Climate Variables for assessing climate variabilityTo updatehttps://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overviewClimate Analysis, Data Sourcecds_essential_variabilityclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables
fates-emerald2.0fates-emeraldTo updateEMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host modelTo updatehttps://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_apiClimate Analysisctsm_fatesclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald
mean-per-zone0.2.0pythonTo updateCreates a png image showing statistic over areas as defined in the vector fileTo updatehttps://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/Visualization, GIS, Climate Analysismean_per_zoneclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone
psy-maps1.2.1pythonTo updateVisualization of regular geographical data on a map with psyplotTo updatehttps://github.com/Chilipp/psy-mapsVisualization, Climate Analysispsy_mapsclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps
shift-longitudes0.1.0pythonTo updateShift longitudes ranging from 0. and 360 degrees to -180. and 180. degreesTo updatehttps://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/Climate Analysisshift_longitudesclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes
smithsonian-volcanoes0.1.0pythonTo updateRetrieve data from Volcanoes of the World (VOTW) DatabaseTo updatehttps://volcano.si.edu/gvp_votw.cfmRetrieve Datasmithsonian_volcanoesclimatehttps://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes
droplet-barcode-plot1.6.1+galaxy20.0.1scxa-plotsTo updateMake a cell barcode plot for droplet single-cell RNA-seq QCTo updatehttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiarySequence Analysisdroplet_barcode_plotebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml
fastq_provider0.4.40.4.7atlas-fastq-providerTo updateRetrieval and download of FASTQ files from ENA and other repositories such as HCA.To updatehttps://github.com/ebi-gene-expression-group/atlas-fastq-providerData Source, RNA, Transcriptomicsatlas_fastq_providerebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider
gtf-2-gene-list1.52.0+galaxy01.1.0atlas-gene-annotation-manipulationTo updateUtility to extract annotations from Ensembl GTF files.To updatehttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiarySequence Analysisgtf2gene_listebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml
fastq_pair1.0+galaxy01.0fastq-pairTo updatePaired-end fastq pairerTo updatehttps://github.com/linsalrob/fastq-pairFastq Manipulationfastq_pairebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair
fastq_quality_trimmer0.0.14+galaxy00.0.14fastx_toolkitTo updateFASTQ trimmer based on qualityTo updatehttps://github.com/agordon/fastx_toolkitFastq Manipulationfastq_quality_trimmerebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer
fastq_utils0.25.1+galaxy00.25.2fastq_utilsTo updateSet of tools for handling fastq filesTo updatehttps://github.com/nunofonseca/fastq_utilsTranscriptomics, RNAfastq_utilsebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils
salmon-kallisto-mtx-to-10x0.0.1+galaxy6scipyTo updateTransforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X dataTo updatehttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiarySequence Analysissalmon_kallisto_mtx_to_10xebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml
cell-types-analysis1.1.10.1.11cell-types-analysisTo updateTools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysisTo updateTranscriptomics, RNA, Statisticssuite_cell_types_analysisebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
data-hcav0.0.4+galaxy00.0.4hca-matrix-downloaderTo updateTools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projectsTo updateTranscriptomics, Sequence Analysissuite_human_cell_atlas_toolsebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
data-scxav0.0.2+galaxy2wgetTo updateTools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/homeTo updateTranscriptomics, Sequence Analysissuite_ebi_expression_atlasebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
decoupler1.4.0+galaxy21.5.0decouplerTo updatedecoupler - Ensemble of methods to infer biological activitiesTo updatehttps://decoupler-py.readthedocs.io/en/latest/Transcriptomicssuite_decouplerebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
dropletutils1.0.40.0.5dropletutils-scriptsTo updateDe-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_dropletutilsebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
garnett0.2.80.0.5garnett-cliTo updateDe-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_garnettebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
monocle30.1.40.0.9monocle3-cliTo updateDe-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_monocle3ebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
sc31.8.00.0.6sc3-scriptsTo updateDe-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_sc3ebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
scanpy1.8.11.1.6scanpy-scriptsTo updatescanpy-scripts, command-line wrapper scripts around Scanpy.To updatehttps://scanpy.readthedocs.ioTranscriptomics, Sequence Analysis, RNAscanpy_scriptsebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy
scater1.10.00.0.5scater-scriptsTo updateDe-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_scaterebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
sccaf0.0.90.0.10sccafTo updateSCCAF: Single Cell Clustering Assessment Framework.To updatehttps://github.com/sccaf/sccafTranscriptomicsSCCAFebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf
sceasy0.0.50.0.7r-sceasyTo updateConvert scRNA data object between popular formatsTo updateTranscriptomicssceasyebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
scmap1.6.30.0.11scmap-cliTo updateDe-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_scmapebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
scpred1.0.20.1.0scpred-cliTo updateDe-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_scpredebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
seurat0.3.04.0.0seurat-scriptsTo updateDe-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1To updateTranscriptomics, RNA, Statistics, Sequence Analysissuite_seuratebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
ucsc-cell-browser1.0.0+galaxy11.2.3ucsc-cell-browserTo updatePython pipeline and Javascript scatter plot library for single-cell datasetsTo updatehttps://cells.ucsc.edu/Transcriptomicsucsc_cell_browserebi-gxahttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml
biotransformer3.0.202304033.0.20230403biotransformerUp-to-datebiotransformerBioTransformerMetabolic pathway prediction, PTM site prediction, Natural product identificationSmall molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMRBioTransformer is a tool for prediction of small molecule metabolism in mammals.BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.Up-to-datehttps://bitbucket.org/djoumbou/biotransformerjar/src/master/Metabolomicsbiotransformerrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer
filter_compounds3.1.12.3.90dev7d621d9openbabelTo updateTool for filtering organometallics/anorganic compounds from a list of compounds.To updatehttps://github.com/RECETOX/galaxytools/Metabolomicsfilter_compoundsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds
matchms0.23.10.23.1matchmsUp-to-datematchmsMatchmsSpectral library search, Format validation, FilteringMetabolomicsSearching, filtering and converting mass spectral libraries.Tool to import, process, clean, and compare mass spectrometry data.Up-to-datehttps://github.com/matchms/matchmsMetabolomicsmatchmsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/matchms
msmetaenhancer0.3.00.3.0msmetaenhancerUp-to-datemsmetaenhancerMSMetaEnhancerAnnotation, Standardisation and normalisationMetabolomics, Compound libraries and screening, Data submission, annotation and curationTool for mass spectra metadata annotation.Up-to-datehttps://github.com/RECETOX/MSMetaEnhancerMetabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer
msp_merge0.1.00.23.1matchmsTo updateTo updatehttps://github.com/RECETOX/galaxytoolsMetabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge
mzml_validator0.1.0+galaxy2lxmlTo updatemzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.To updatehttps://github.com/RECETOX/galaxytoolsMetabolomics, Proteomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator
query0.2clickTo updateExecute an SQL statement on a set of tablesTo updateText Manipulationqueryrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/query
ramclustr1.3.01.3.1r-ramclustrTo updateramclustrRAMClustRImputation, Standardisation and normalisation, Clustering, CorrelationMetabolomicsA feature clustering algorithm for non-targeted mass spectrometric metabolomics data.To updatehttps://rdrr.io/cran/RAMClustR/Metabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr
recetox_aplcms0.12.00.12.0r-recetox-aplcmsUp-to-daterecetox-aplcmsrecetox-aplcmsChromatographic alignment, Quantification, Peak detection, Feature extraction, AlignmentMetabolomicsPeak detection tool for HRMS profile data.recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening.Up-to-datehttps://github.com/RECETOX/recetox-aplcmsMetabolomicsrecetox-aplcmsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms
recetox_msfinderv3.5.2To updaterecetox-msfinderrecetox-msfinderAnnotationMetabolomicsThis is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0.To updatehttps://github.com/RECETOX/recetox-msfinderMetabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder
recetox_xmsannotator0.10.00.10.0r-recetox-xmsannotatorUp-to-daterecetox-xmsannotatorrecetox-xMSannotatorExpression profile pathway mapping, Structure comparison, Isotopic distributions calculation, AnnotationAnnotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring.Up-to-datehttps://github.com/RECETOX/recetox-xMSannotatorMetabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator
retip0.5.4To updateretipRetipRetention time prediction, Spectrum calculation, Deisotoping, Formatting, DepositionMetabolomics, Proteomics experiment, Machine learning, Cheminformatics, ChemistryRetention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.To updatehttps://github.com/PaoloBnn/RetipMetabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/retip
riassigner0.3.40.3.4riassignerUp-to-dateriassignerRIAssignerStandardisation and normalisationMetabolomics, Compound libraries and screening, Data submission, annotation and curationRIAssigner is a python tool for retention index (RI) computation for GC-MS data.Up-to-datehttps://github.com/RECETOX/RIAssignerMetabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/riassigner
rmassbank3.0.0pythonTo updateRMassBank is an R package for processing tandem MS files and building of MassBank records.To updatehttps://github.com/MassBank/RMassBankMetabolomicsrmassbankrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank
spec2vec0.8.00.8.0spec2vecUp-to-datespec2vecSpec2VecSpectrum calculation, Spectral library search, Database search, Natural product identificationProteomics experiment, Metabolomics, Natural language processing, ProteomicsMass spectra similarity scoring using a trained Spec2Vec model.Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set.Up-to-datehttps://github.com/iomega/spec2vecMetabolomicsspec2vecrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec
waveica0.2.00.2.0r-recetox-waveicaUp-to-datewaveicaWaveICAStandardisation and normalisationMetabolomicsRemoval of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform.Up-to-datehttps://github.com/RECETOX/WaveICAMetabolomicsrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/waveica
xtb6.6.1xtbTo updatePerforms semiempirical molecular optimization.To updatehttps://github.com/grimme-lab/xtbMetabolomicsxtb_molecular_optimizationrecetoxhttps://github.com/RECETOX/galaxytools/tree/master/tools/xtb
consolidate_vcfs1.8.21.8.2snvphyl-toolsUp-to-dateCombines freebayes and mpileup files for use by vcf2snvalignmentUp-to-datehttps://snvphyl.readthedocs.io/en/latest/Sequence Analysisconsolidate_vcfsnmlhttps://github.com/phac-nml/snvphyl-galaxy
filter_density1.8.21.8.2snvphyl-toolsUp-to-dateFilter out position based on distance between SNVsUp-to-datehttps://snvphyl.readthedocs.io/en/latest/Sequence Analysisfilter_densitynmlhttps://github.com/phac-nml/snvphyl-galaxy
filter_stats1.8.21.8.2snvphyl-toolsUp-to-dateSNVPhyl filter_statsUp-to-datehttps://snvphyl.readthedocs.io/en/latest/Sequence Analysisfilter_statsnmlhttps://github.com/phac-nml/snvphyl-galaxy
filter_vcf1.8.21.8.2snvphyl-toolsUp-to-dateSNVPhyl filter_vcfUp-to-datehttps://snvphyl.readthedocs.io/en/latest/Sequence Analysisfilter_vcfnmlhttps://github.com/phac-nml/snvphyl-galaxy
find_repeats1.8.21.8.2snvphyl-toolsUp-to-dateFind repetitive regions on a reference genome using MUMMerUp-to-datehttps://snvphyl.readthedocs.io/en/latest/Sequence Analysisfind_repeatsnmlhttps://github.com/phac-nml/snvphyl-galaxy
positions2snv_alignment1.8.21.8.2snvphyl-toolsUp-to-dateGenerate alignment of SNVs from SNVPhyl variant table.Up-to-datehttps://snvphyl.readthedocs.io/en/latest/Variant Analysispositions2snv_alignmentnmlhttps://github.com/phac-nml/snvphyl-galaxy
positions2snv_invariant_alignment1.8.21.8.2snvphyl-toolsUp-to-dateGenerate alignment of SNVs and non-variant positions from SNVPhyl variant table.Up-to-datehttps://snvphyl.readthedocs.io/en/latest/Variant Analysispositions2snv_invariant_alignmentnmlhttps://github.com/phac-nml/snvphyl-galaxy
snv_matrix1.8.21.8.2snvphyl-toolsUp-to-dateGenerate matrix of SNV distancesUp-to-datehttps://snvphyl.readthedocs.io/en/latest/Sequence Analysissnv_matrixnmlhttps://github.com/phac-nml/snvphyl-galaxy
vcf2snvalignment1.8.21.8.2snvphyl-toolsUp-to-dateGenerates multiple alignment of variant callsUp-to-datehttps://snvphyl.readthedocs.io/en/latest/Sequence Analysisvcf2snvalignmentnmlhttps://github.com/phac-nml/snvphyl-galaxy
verify_map1.8.21.8.2snvphyl-toolsUp-to-dateChecks the mapping quality of all BAM(s)Up-to-datehttps://snvphyl.readthedocs.io/en/latest/Sequence Analysisverify_mapnmlhttps://github.com/phac-nml/snvphyl-galaxy
suite_snvphylTo updateSNVPhyl suite defining all dependencies for SNVPhylTo updateSequence Analysissuite_snvphyl_1_2_3nmlhttps://github.com/phac-nml/snvphyl-galaxy
cooler0.9.31.18htslibTo updatecooler different tools to process Hi-C from mirnylabTo updatehttps://github.com/open2c/coolerEpigeneticscoolerlldelislehttps://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml
fromHicupToJuicebox0.0.20.22.0pysamTo updateConvert the output of hicup (as sam or bam) to the input of juicebox.To updateEpigeneticsfrom_hicup_to_juiceboxlldelisle
fromgtfTobed120.11.1+galaxy00.12gffutilsTo updateConvert GTF files to BED12 formatTo updatehttps://pythonhosted.org/gffutils/contents.htmlConvert Formatsfromgtftobed12lldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12
getTn5ExtendedCoverage0.0.20.22.0pysamTo updateTake an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extensionTo updateEpigeneticsgettn5extendedcoveragelldelisle
hyperstack_to_bleach_corrected_movie2023032820220414FijiTo updateGenerate blach corrected movie from hyperstackTo updateImaginghyperstack_to_bleach_corrected_movielldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie
incucyte_stack_and_upload_omero2023082420220414FijiTo updateCombine images to stack and upload to the omero serverTo updateImagingincucyte_stack_and_upload_omerolldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero
measure_gastruloids2022121620220414fijiTo updateGet the ROI coordinates around the gastruloids as well as measurements like Area, elongation indexTo updateImagingmeasure_gastruloidslldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids
omero_clean_rois_tables2023062320220414fijiTo updateRemove all ROIs and all tables on OMERO associated to an omero object and recursively up and downTo updateImagingomero_clean_rois_tableslldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables
omero_hyperstack_to_fluo_measurements_on_gastruloid2023080920220414fijiTo updateAnalyse Hyperstack on OMERO server to measure fluorescence levelsTo updateImagingomero_hyperstack_to_fluo_measurements_on_gastruloidlldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid
omero_hyperstack_to_gastruloid_measurements2023072820220414fijiTo updateAnalyse Hyperstack on OMERO server to segment gastruloid and compute measurementsTo updateImagingomero_hyperstack_to_gastruloid_measurementslldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements
revertR2orientationInBam0.0.21.18samtoolsTo updateRevert the mapped orientation of R2 mates in a bam.To updateSAMrevertr2orientationinbamlldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam
upload_roi_and_measures_to_omero0.0.55.11.1omero-pyTo updateUpload the ROI coordinates and the measurements to the omero serverTo updateImagingupload_roi_and_measures_to_omerolldelislehttps://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero
+ +
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