Snakemake-Workflows
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Repositories
- dna-seq-benchmark Public
A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets
- single-cell-counts-preprocessing Public
A standardised Snakemake workflow for preprocessing of single-cell RNAseq count data following single-cell best practices.
- dna-seq-varlociraptor Public
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.
- rna-longseq-de-isoform Public
long read differential expression analysis and splice variant analysis
- rna-seq-kallisto-sleuth Public
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
- dna-seq-mtb Public
A flavor of https://github.com/snakemake-workflows/dna-seq-varlociraptor preconfigured for molecular tumor boards
- cellranger-multi Public
A Snakemake workflow for preprocessing single cell RNAseq (scRNA-seq) data with `cellranger multi` (Cell Ranger licensing requires a manual download of the software).
- rna-seq-xengsort Public
A standardized Snakemake workflow to separate host and graft sequencing reads from RNAseq data using xengsort.
- read-alignment-pangenome Public
Standardized snakemake workflow for aligning sequencing reads to a pangenome.
- star-arriba-fusion-calling Public
A standardized snakemake workflow to map RNAseq reads with star and call fusions on the resulting alignment files with arriba.
