GroopM: An automated tool for the recovery of population genomes from related metagenomes
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Published
- Accepted
- Subject Areas
- Bioinformatics, Genomics, Microbiology
- Keywords
- Metagenomics, Population genome binning, Bioinformatics, Microbial ecology
- Copyright
- © 2014 Imelfort et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2014. GroopM: An automated tool for the recovery of population genomes from related metagenomes. PeerJ PrePrints 2:e409v1 https://doi.org/10.7287/peerj.preprints.409v1
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.
Supplemental Information
Supplementary materials
The Supplementary materials file contains all supplementary methods, notes, figures, and tables referenced in the main text.