Introduction

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.

Publications

  1. GroopM: an automated tool for the recovery of population genomes from related metagenomes.
    Cite this
    Imelfort M, Parks D, Woodcroft BJ, Dennis P, Hugenholtz P, Tyson GW, 2014-01-01 - PeerJ

Credits

  1. Michael Imelfort
    Developer

    Australian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, Australia

  2. Donovan Parks
    Developer

    Australian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, Australia

  3. Ben J Woodcroft
    Developer

    Australian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, Australia

  4. Paul Dennis
    Developer

    Australian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, Australia

  5. Philip Hugenholtz
    Developer

    Australian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, Australia

  6. Gene W Tyson
    Investigator

    Australian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, Australia

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Summary
AccessionBT000457
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionAustralia
Submitted ByGene W Tyson