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.

Features

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.

Installation

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

Contribute

• Issue Tracker: github
• Source Code: github

Support

If you are having issues, please let us know. We have a discussion thread on gitter:

Known Issues

• Contig names consisting of digits only are not allowed. Please rename your contigs in both the fasta and the coverage table before proceeding.
• Contig sequences can only contain letters A,C,G or T. For example Ns are currently not allowed.
• Contigs need to be cut up prior to binning. This is covered in the Basic Usage page.

For a more up to date list of reported issues, check the issue tracker: https://github.com/BinPro/CONCOCT/issues

Licence

FreeBSD

Contents:

• CONCOCT’s documentation
• Installation
  • With Bioconda [Recommended]
  • Manual Installation
  • Using Docker
  • Other Programs Needed
• Basic Usage
• Command Line Options
• CONCOCT Scripts
  • cut_up_fasta.py
  • concoct_coverage_table.py
  • merge_cutup_clustering.py
  • extract_fasta_bins.py
  • dnadiff_dist_matrix.py
  • [Deprecated] extract_scg_bins.py

Indices and tables

• Index
• Module Index
• Search Page