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

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

Supplementar

SUBMITTER: Stewart RD 

PROVIDER: S-EPMC6581432 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature