Binning metagenomic contigs by coverage and composition

doi:10.1038/nmeth.3103

. 2014 Nov;11(11):1144-6.

doi: 10.1038/nmeth.3103. Epub 2014 Sep 14.

Binning metagenomic contigs by coverage and composition

Affiliations

¹ 1] KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden. [2].
² 1] KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden. [2] Bioinformatics Infrastructure for Life Sciences (BILS), Stockholm, Sweden.
³ School of Engineering, University of Glasgow, Glasgow, UK.
⁴ 1] Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK. [2] National Institute for Health Research Surgical Reconstruction (NIHR) Surgical Reconstruction and Microbiology Research Centre, University of Birmingham, UK.
⁵ 1] Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland. [2] Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands.
⁶ Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
⁷ 1] School of Engineering, University of Glasgow, Glasgow, UK. [2].

PMID: 25218180
DOI: 10.1038/nmeth.3103

Binning metagenomic contigs by coverage and composition

Johannes Alneberg et al. Nat Methods. 2014 Nov.

. 2014 Nov;11(11):1144-6.

doi: 10.1038/nmeth.3103. Epub 2014 Sep 14.

Authors

Affiliations

¹ 1] KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden. [2].
² 1] KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden. [2] Bioinformatics Infrastructure for Life Sciences (BILS), Stockholm, Sweden.
³ School of Engineering, University of Glasgow, Glasgow, UK.
⁴ 1] Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK. [2] National Institute for Health Research Surgical Reconstruction (NIHR) Surgical Reconstruction and Microbiology Research Centre, University of Birmingham, UK.
⁵ 1] Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland. [2] Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands.
⁶ Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
⁷ 1] School of Engineering, University of Glasgow, Glasgow, UK. [2].

PMID: 25218180
DOI: 10.1038/nmeth.3103

Abstract

Shotgun sequencing enables the reconstruction of genomes from complex microbial communities, but because assembly does not reconstruct entire genomes, it is necessary to bin genome fragments. Here we present CONCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatically cluster contigs into genomes. We demonstrate high recall and precision on artificial as well as real human gut metagenome data sets.

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References

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[1] Nature. 2012 Jun 13;486(7402):207-14 - PubMed

[2] Nature. 2012 Jun 13;486(7402):207-14 - PubMed

[3] BMC Bioinformatics. 2009 Oct 02;10:316 - PubMed

[4] BMC Bioinformatics. 2009 Oct 02;10:316 - PubMed

[5] mBio. 2013 May 28;4(3):e00569-12 - PubMed

[6] mBio. 2013 May 28;4(3):e00569-12 - PubMed

[7] Nature. 2004 Mar 4;428(6978):37-43 - PubMed

[8] Nature. 2004 Mar 4;428(6978):37-43 - PubMed

[9] Genome Res. 2001 Aug;11(8):1404-9 - PubMed

[10] Genome Res. 2001 Aug;11(8):1404-9 - PubMed

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Binning metagenomic contigs by coverage and composition

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Binning metagenomic contigs by coverage and composition

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