SnakeWRAP: a Snakemake workflow to facilitate automated processing of metagenomic data through the metaWRAP pipeline

Abstract

Generating high-quality genome assemblies of complex microbial populations from shotgun metagenomics data is often a manually intensive task involving many computational steps. SnakeWRAP is a novel tool, implemented in the Snakemake workflow language, to automate multiple metaWRAP modules. Specifically, it wraps the shell scripts provided within the original metaWRAP software, within Snakemake. This approach enables high-throughput simultaneous assembly and analysis of multiple shotgun metagenomic datasets using the robust modular metaWRAP software. We expect this advancement to be of import in institutions where high-performance computing infrastructure is available, especially in the context of big data. This software tool is publicly available at https://github.com/jkrapohl/SnakeWRAP.

Keywords: Snakemake; big data; high-performance computing; metaWRAP; shotgun metagenomics.