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

Research output: Contribution to journalArticlepeer-review

540 Citations (Scopus)


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)1144-6
Number of pages3
JournalNature Methods
Issue number11
Publication statusPublished - Nov 2014


  • Algorithms
  • Bifidobacterium
  • Contig Mapping
  • Escherichia coli K12
  • Feces
  • Gastrointestinal Tract
  • Genome, Bacterial
  • Humans
  • Metagenome
  • Metagenomics
  • Microbiota
  • Sequence Analysis, DNA
  • Shiga-Toxigenic Escherichia coli
  • Software


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