grenepipe: a flexible, scalable and reproducible pipeline to automate variant calling from sequence reads
Lucas Czech, Moisés Expósito‐Alonso
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.
Topics & Concepts
WorkflowComputer scienceScalabilityPipeline (software)SoftwareThroughputFile formatSequence (biology)Data miningDatabaseOperating systemDistributed computingBiologyWirelessGeneticsGenomics and Phylogenetic StudiesScientific Computing and Data ManagementGene expression and cancer classification