Snakemake-Workflows

A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets

A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.

A flavor of https://github.com/snakemake-workflows/dna-seq-varlociraptor preconfigured for molecular tumor boards

long read differential expression analysis and splice variant analysis

A Snakemake workflow for preprocessing single cell RNAseq (scRNA-seq) data with `cellranger multi` (Cell Ranger licensing requires a manual download of the software).

A standardized Snakemake workflow to separate host and graft sequencing reads from RNAseq data using xengsort.

A standardised Snakemake workflow for preprocessing of single-cell RNAseq count data following single-cell best practices.

Standardized snakemake workflow for aligning sequencing reads to a pangenome.

A standardized snakemake workflow to map RNAseq reads with star and call fusions on the resulting alignment files with arriba.

A template for standard compliant snakemake-workflows