MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis

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.