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

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 cover...

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Detalles Bibliográficos
Autores principales: Imelfort, Michael, Parks, Donovan, Woodcroft, Ben J., Dennis, Paul, Hugenholtz, Philip, Tyson, Gene W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183954/
https://www.ncbi.nlm.nih.gov/pubmed/25289188
http://dx.doi.org/10.7717/peerj.603
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author Imelfort, Michael
Parks, Donovan
Woodcroft, Ben J.
Dennis, Paul
Hugenholtz, Philip
Tyson, Gene W.
author_facet Imelfort, Michael
Parks, Donovan
Woodcroft, Ben J.
Dennis, Paul
Hugenholtz, Philip
Tyson, Gene W.
author_sort Imelfort, Michael
collection PubMed
description 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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spelling pubmed-41839542014-10-06 GroopM: an automated tool for the recovery of population genomes from related metagenomes Imelfort, Michael Parks, Donovan Woodcroft, Ben J. Dennis, Paul Hugenholtz, Philip Tyson, Gene W. PeerJ Bioinformatics 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. PeerJ Inc. 2014-09-30 /pmc/articles/PMC4183954/ /pubmed/25289188 http://dx.doi.org/10.7717/peerj.603 Text en © 2014 Imelfort et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , 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) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Imelfort, Michael
Parks, Donovan
Woodcroft, Ben J.
Dennis, Paul
Hugenholtz, Philip
Tyson, Gene W.
GroopM: an automated tool for the recovery of population genomes from related metagenomes
title GroopM: an automated tool for the recovery of population genomes from related metagenomes
title_full GroopM: an automated tool for the recovery of population genomes from related metagenomes
title_fullStr GroopM: an automated tool for the recovery of population genomes from related metagenomes
title_full_unstemmed GroopM: an automated tool for the recovery of population genomes from related metagenomes
title_short GroopM: an automated tool for the recovery of population genomes from related metagenomes
title_sort groopm: an automated tool for the recovery of population genomes from related metagenomes
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183954/
https://www.ncbi.nlm.nih.gov/pubmed/25289188
http://dx.doi.org/10.7717/peerj.603
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