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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2014
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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. |
format | Online Article Text |
id | pubmed-4183954 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
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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