Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

ChIP-seq peak-calling, QC and differential analysis pipeline.

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair

NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads

Reference-based consensus creation

Nextflow DSL2 pipeline to generate a Genome Note, including assembly statistics, quality metrics, and Hi-C contact maps. This workflow is part of the Tree of Life production suite.