Metagenome-Atlas is a easy-to-use metagenomic pipeline based on snakemake
It handels all steps from QC, Assembly, Binning, to Annotation.
Three commands to start analysing your metagenome data:
conda install -y -c bioconda -c conda-forge metagenome-atlas
atlas init --db-dir databases path/to/fastq/files
atlas run all
All databases and dependencies are installed on the fly. Atlas is based on snakemake which allows to sheddule parts of the workflow to a cluster.
Have a Look
You want to run these three commands on the example data.
Atlas should be run on a linux sytem, with enough memory (min ~50GB but assembly usually requires 250GB). The only dependency is the conda package manager, which can easy be installed with anaconda.
If you have more time, then we recommend you to create a conda environment for atlas to avoid any conflicts of versions.
conda create -y -n atlasenv
source activate atlasenv
conda install -y -c bioconda -c conda-forge metagenome-atlas
And you can run atlas. All other dependencies are installed in specific environments during the run of the pipeline.
We recommend you configure atlas according to your needs.
- check the
samples.tsv - edit the
config.yaml - run atlas on any cluster system
For local execution we have also a docker container
We have a BioRxiv preprint please cite:
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data Silas Kieser, Joseph Brown, Evgeny M Zdobnov, Mirko Trajkovski, Lee Ann McCue bioRxiv 737528; doi: https://doi.org/10.1101/737528