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

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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Bibliographic Details
Main Authors: Michael Imelfort, Donovan Parks, Ben J. Woodcroft, Paul Dennis, Philip Hugenholtz, Gene W. Tyson
Format: Article
Language:English
Published: PeerJ Inc. 2014-09-01
Series:PeerJ
Subjects:
Metagenomics
Population genome binning
Bioinformatics
Microbial ecology
Online Access:https://peerj.com/articles/603.pdf
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spelling doaj-4fb3da2c6c4c446b931486292be06fbd2020-11-24T22:43:08ZengPeerJ Inc.PeerJ2167-83592014-09-012e60310.7717/peerj.603603GroopM: an automated tool for the recovery of population genomes from related metagenomesMichael Imelfort0Donovan Parks1Ben J. Woodcroft2Paul Dennis3Philip Hugenholtz4Gene W. Tyson5Australian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, AustraliaAustralian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, AustraliaAustralian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, AustraliaAustralian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, AustraliaAustralian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, AustraliaAustralian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, AustraliaMetagenomic 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.https://peerj.com/articles/603.pdfMetagenomicsPopulation genome binningBioinformaticsMicrobial ecology
collection DOAJ
language English
format Article
sources DOAJ
author Michael Imelfort
Donovan Parks
Ben J. Woodcroft
Paul Dennis
Philip Hugenholtz
Gene W. Tyson
spellingShingle Michael Imelfort
Donovan Parks
Ben J. Woodcroft
Paul Dennis
Philip Hugenholtz
Gene W. Tyson
GroopM: an automated tool for the recovery of population genomes from related metagenomes
PeerJ
Metagenomics
Population genome binning
Bioinformatics
Microbial ecology
author_facet Michael Imelfort
Donovan Parks
Ben J. Woodcroft
Paul Dennis
Philip Hugenholtz
Gene W. Tyson
author_sort Michael Imelfort
title 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_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_sort groopm: an automated tool for the recovery of population genomes from related metagenomes
publisher PeerJ Inc.
series PeerJ
issn 2167-8359
publishDate 2014-09-01
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.
topic Metagenomics
Population genome binning
Bioinformatics
Microbial ecology
url https://peerj.com/articles/603.pdf
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AT pauldennis groopmanautomatedtoolfortherecoveryofpopulationgenomesfromrelatedmetagenomes
AT philiphugenholtz groopmanautomatedtoolfortherecoveryofpopulationgenomesfromrelatedmetagenomes
AT genewtyson groopmanautomatedtoolfortherecoveryofpopulationgenomesfromrelatedmetagenomes
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