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PeerJ. 2014 Sep 30;2:e603. doi: 10.7717/peerj.603. eCollection 2014.

GroopM: an automated tool for the recovery of population genomes from related metagenomes.

Author information

1
Australian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD , Australia.
2
Australian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD , Australia ; Advanced Water Management Center (AWMC), The University of Queensland , St Lucia, QLD , Australia.

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.

KEYWORDS:

Bioinformatics; Metagenomics; Microbial ecology; Population genome binning

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