MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs)

Information
Authors: 
Stewart, R., Auffret, M. D., Snelling, T. J., Roehe, R. & Watson, M.
Journal: 
Bioinformatics
Journal publication date: 
2018
DOIs: 
https://doi.org/10.1093/bioinformatics/bty905
Abstract

Motivation: Metagenomics is a powerful tool for assaying the DNA from every genome present in an environment. Recent advances in bioinformatics have enabled the rapid assembly of near complete metagenome-assembled genomes (MAGs), and there is a need for reproducible pipelines that can annotate and characterise thousands of genomes simultaneously, to enable identification and functional characterisation. Results: Here we present MAGpy, a scalable and reproducible pipeline that takes multiple genome assemblies as FASTA and compares them to several public databases, checks quality, suggests a taxonomy and draws a phylogenetic tree. Availability: MAGpy is available on github: https://github.com/WatsonLab/MAGpy Contact:mick.watson@roslin.ed.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.