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

Abstract

AbstractSummaryWe 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 implementationgrenepipe is published under the GPLv3 and freely available at github.com/moiexpositoalonsolab/grenepipe.