MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs)
2019
Stewart, Robert D. | Birol, Inanc | Auffret, Marc D | Snelling, Timothy J | Roehe, Rainer | Watson, Mick
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. 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. MAGpy is available on github: https://github.com/WatsonLab/MAGpy. Supplementary data are available at Bioinformatics online.
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