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

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    Rights statement: © The Author(s) 2018. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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

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.

ID: 76532746