Binning metagenomic contigs by coverage and composition

Johannes Alneberg, Brynjar Smári Bjarnason, Ino De Bruijn, Melanie Schirmer, Joshua Quick, Umer Z. Ijaz, Leo Lahti, Nicholas J. Loman, Anders F. Andersson*, Christopher Quince

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

618 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)1144-1146
Number of pages3
JournalNature Methods
Volume11
Issue number11
DOIs
Publication statusPublished - 30 Oct 2014
Externally publishedYes

Bibliographical note

Funding Information:
This research arose out of a workshop funded through the COST project ES1103 and hosted by P. Fernandes at the Instituto Gulbenkian de Ciência. This work was funded by grants (to A.F.A.) from the Swedish Research Councils VR (grant 2011-5689), FORMAS (grant 2009-1174) and EC BONUS project BLUEPRINT. C.Q. is funded by an EPSRC Career Acceleration Fellowship—EP/H003851/1. M.S. is supported by Unilever R&D Port Sunlight, Bebington, UK. L.L. is supported by the Academy of Finland (grant 256950), N.L. by a UK Medical Research Council Special Training Fellowship in Biomedical Informatics and J.Q. by the UK National Institute for Health Research (NIHR) Centre for Surgical Reconstruction and Microbiology. This paper presents independent research funded by the NIHR Surgical Reconstruction and Microbiology Research Centre (partnership between University Hospitals Birmingham National Health Service (NHS) Foundation Trust, the University of Birmingham and the Royal Centre for Defence Medicine). The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health.

Publisher Copyright:
© 2014 Nature America, Inc.

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