GroopM: an Automated Tool for the Recovery of Population Genomes from Related Metagenomes

Overview

Journal PeerJ

Specialties Biology
Environmental Health
General Medicine

Date 2014 Oct 8

PMID 25289188

Citations 135

Authors

Michael Imelfort

Donovan Parks

Ben J Woodcroft

Paul Dennis

Philip Hugenholtz

Gene W Tyson

Affiliations

Soon will be listed here.

Abstract

Metagenomic binning methods that leverage differential population abundances in microbial communities (differential coverage) are emerging as a complementary approach to conventional composition-based binning. Here we introduce GroopM, an automated binning tool that primarily uses differential coverage to obtain high fidelity population genomes from related metagenomes. We demonstrate the effectiveness of GroopM using synthetic and real-world metagenomes, and show that GroopM produces results comparable with more time consuming, labor-intensive methods.

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