Journal article
MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis
Babak Shaban, Mar Quiroga, Robert Turnbull, Edoardo Tescari, Kim-Anh Lê Cao, Heroen Verbruggen
Journal of Open Source Software | The Open Journal | Published : 2023
DOI: 10.21105/joss.04851
Abstract
MetaGenePipe (MGP) is an efficient, flexible, portable, and scalable metagenomics pipeline that uses performant bioinformatics software suites and genomic databases to create an accurate taxonomic and functional characterization of the prokaryotic fraction of sequenced microbiomes. Written in the Workflow Definition Language (WDL), MGP produces output that can be explored and interpreted directly, or can be used for downstream analysis. MGP is a pipeline-development best practice tool that uses Singularity for containerization and includes a setup script that downloads the necessary databases for setup. The source code for MGP is freely available and distributed under the Apache 2.0 license.