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

Robert D Stewart, Marc Auffret, Timothy J Snelling, Rainer Roehe, Mick Watson

Research output: Contribution to journalArticle

3 Citations (Scopus)
15 Downloads (Pure)

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.

Supplementary information: Supplementary data are available at Bioinformatics online.

Original languageEnglish
Article numberbty905
Number of pages3
JournalBioinformatics
Early online date10 Nov 2018
DOIs
Publication statusFirst published - 10 Nov 2018

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Metagenome
Genome
Computational Biology
Metagenomics
Databases
DNA

Cite this

Stewart, Robert D ; Auffret, Marc ; Snelling, Timothy J ; Roehe, Rainer ; Watson, Mick. / MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs). In: Bioinformatics. 2018.
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MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs). / Stewart, Robert D; Auffret, Marc; Snelling, Timothy J; Roehe, Rainer; Watson, Mick.

In: Bioinformatics, 10.11.2018.

Research output: Contribution to journalArticle

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