CONCOCT’s documentation

CONCOCT “bins” metagenomic contigs. Metagenomic binning is the process of clustering sequences into clusters corresponding to operational taxonomic units of some level.

For any known issues with CONCOCT check the issue tracker:


CONCOCT does unsupervised binning of metagenomic contigs by using nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately (up to species level) bin metagenomic contigs. For optimal performance:

  • Map several samples against your assembled contigs.
  • Cut longer contigs into 10 - 20 kb pieces prior to mapping.
  • Evaluate your bins using single copy genes.


For a comprehensive guide on how to install CONCOCT and all its dependencies, see Installation.



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