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Article

grenepipe: a flexible, scalable and reproducible pipeline to automate variant calling from sequence reads.

Bioinformatics (Oxford, England) - 14 Oct 2022

Czech Lucas, Exposito-Alonso Moises

Abstract excerpt

SUMMARY: We developed grenepipe, an all-in-one Snakemake workflow to streamline the data processing from raw high-throughput sequencing data of individuals or populations to genotype variant calls. Our pipeline offers a range of popular software tools within a single configuration file, automatically installs software dependencies, is highly optimized for scalability in cluster environments and runs with a single...

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PMID: 36053180
DOI: 10.1093/bioinformatics/btac600
PMCID: PMC10424805

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