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.
© The Author(s) 2018. Published by Oxford University Press.