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

• DOI: 10.1093/bioinformatics/btac600
• Publication Date: 2022-09-02T13:58:40Z
• Authors: Lucas Czech; Moises Exposito-A...
• Keywords: 0301 basic medicine; 03 medical and health sciences; Genotype; High-Throughput Nucleotide Sequencing; Humans; Software; Workflow

Abstract

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 command.

Availability and implementation grenepipe is published under the GPLv3 and freely available at github.com/moiexpositoalonsolab/grenepipe.