Binning metagenomic contigs by coverage and composition

Alneberg, J., Bjarnason, B. S., de Bruijn, I., Schirmer, M., Quick, J., Ijaz, U. Z. , Lahti, L., Loman, N. J., Andersson, A. F. and Quince, C. (2014) Binning metagenomic contigs by coverage and composition. Nature Methods, 11(11), pp. 1144-1146. (doi:10.1038/NMETH.3103) (PMID:25218180)

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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.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Schirmer, Ms Melanie and Quince, Dr Christopher and Ijaz, Dr Umer Zeeshan
Authors: Alneberg, J., Bjarnason, B. S., de Bruijn, I., Schirmer, M., Quick, J., Ijaz, U. Z., Lahti, L., Loman, N. J., Andersson, A. F., and Quince, C.
College/School:College of Science and Engineering > School of Engineering
College of Science and Engineering > School of Engineering > Electronics and Nanoscale Engineering
College of Science and Engineering > School of Engineering > Infrastructure and Environment
Journal Name:Nature Methods
Publisher:Nature Publishing Group
ISSN:1548-7091
ISSN (Online):1548-7105
Related URLs:

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
503351Pioneering the genomics era of environmental microbiologyChristopher QuinceEngineering & Physical Sciences Research Council (EPSRC)EP/H003851/1ENG - ENGINEERING INFRASTRUCTURE & ENVIR