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- Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
- Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
- Assembly and binning of metagenomes
- Call and score variants from WGS/WES of rare disease patients.
- Parallelised and automated construction of metagenomic classifier databases of different tools
website
Public- Amplicon sequencing analysis workflow using DADA2 and QIIME2
variantbenchmarking
Publicpixelator
PublicPipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)demultiplex
PublicDemultiplexing pipeline for sequencing dataconfigs
PublicConfig files used to define parameters specific to compute environments at different Institutionsmethylarray
PublicProcess methylation data from Illumina arrays. Pre-processing, quality checks, confounder check and DMPs (differentially methylated positions) and DMRs (differentially methylated regions). Optionally estimates cell type composition and adjusts data for it.rangeland
PublicPipeline for remotely sensed imagery. The pipeline processes satellite imagery alongside auxiliary data in multiple steps to arrive at a set of trend files related to land-cover changes.demo
Public- A fully reproducible and state-of-the-art ancient DNA analysis pipeline
- circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
crisprseq
PublicA pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).metapep
Public- A single-cell RNAseq pipeline for 10X genomics data