Snakemake-exome

Snakemake-exome is a snakemake workflow that generates alignments from exome sequencing data (or similar targeted DNA-sequencing data). The workflow is designed to handle paired-end (and optionally multi-lane) sequencing data. Processing of patient-derived xenograft (PDX) samples is also supported, by using disambiguate to separate graft/host sequence reads.

If you use this workflow in a paper, don’t forget to give credits to the authors by citing the URL of this repository and, if available, its DOI (see above).