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

Robert Stewart, Marc D. Auffret, Tim J. Snelling, Rainer Roehe, Michael Watson

Research output: Contribution to journalArticlepeer-review

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.
Original languageEnglish
JournalBioinformatics
Early online date10 Nov 2018
DOIs
Publication statusE-pub ahead of print - 10 Nov 2018

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