title: Binning metagenomic contigs by coverage and composition.
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.
authors.affiliation: 1] KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden. [2].
authors.forename: Johannes
authors.initials: J
authors.lastname: Alneberg
authors.affiliation: 1] KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden. [2].
authors.forename: Brynjar Smári
authors.initials: BS
authors.lastname: Bjarnason
authors.affiliation: 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.
authors.forename: Ino
authors.initials: I
authors.lastname: de Bruijn
authors.affiliation: School of Engineering, University of Glasgow, Glasgow, UK.
authors.forename: Melanie
authors.initials: M
authors.lastname: Schirmer
authors.affiliation: 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.
authors.forename: Joshua
authors.initials: J
authors.lastname: Quick
authors.affiliation: School of Engineering, University of Glasgow, Glasgow, UK.
authors.forename: Umer Z
authors.initials: UZ
authors.lastname: Ijaz
authors.affiliation: 1] Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland. [2] Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands.
authors.forename: Leo
authors.identifier: 000000015537637X
authors.initials: L
authors.lastname: Lahti
authors.affiliation: Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Loman
authors.affiliation: 1] KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden. [2].
authors.forename: Anders F
authors.initials: AF
authors.lastname: Andersson
authors.affiliation: 1] School of Engineering, University of Glasgow, Glasgow, UK. [2].
authors.forename: Christopher
authors.initials: C
authors.lastname: Quince
mesh_terms: D000465:Algorithms; D001644:Bifidobacterium / Q000235:genetics; D020451:Contig Mapping / Q000379:methods*; D048168:Escherichia coli K12 / Q000235:genetics; D005243:Feces / Q000382:microbiology; D041981:Gastrointestinal Tract / Q000382:microbiology*; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D054892:Metagenome / Q000235:genetics*; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D054323:Shiga-Toxigenic Escherichia coli / Q000235:genetics; D012984:Software