MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs).
Ontology highlight
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 characterize thousands of genomes simultaneously, to enable identification and functional characterization.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 and implementation
MAGpy is available on github: https://github.com/WatsonLab/MAGpy.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Stewart RD
PROVIDER: S-EPMC6581432 | biostudies-literature | 2019 Jun
REPOSITORIES: biostudies-literature
Publications
MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs).
Stewart Robert D RD Auffret Marc D MD Snelling Timothy J TJ Roehe Rainer R Watson Mick M
Bioinformatics (Oxford, England) 20190601 12
<h4>Motivation</h4>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 characterize thousands of genomes simultaneously, to enable identification and functional characterization.<h4>Results</h4>Here we present MAGpy, a scalable and reproducible pipeline that takes ...[more]
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