CONCOCT - Clustering cONtigs with COverage and ComposiTion
Metagenomic binning is the task of clustering metagenomic sequences into ‘bins’ corresponding to coherent taxonomical units. CONCOCT performs unsupervised binning of metagenomic contigs using nucleotide composition and coverage data in multiple samples.
The binning is achieved by fitting a Gaussian Mixture Model and can be evaluated using single copy genes through an additional script. The main program is implemented in C and Python as a simple command line utility.
$ concoct --composition_file contigs.fa --coverage_file coverage_table.tsv -b concoct_output/
For the most comprehensive information about the usage and function of CONCOCT so far, see the complete example.
For up to date instructions for installation, see github.
The logo is a derivative from an original by Norma Umer.
Dr Christopher Quince (chrisquince)
Johannes Alneberg (alneberg)
Brynjar Smari Bjarnasson (binnisb)
Ino de Bruijn (inodb)
Dr Umer Zeeshan Ijaz (umerijaz)
Dr Nick Loman (nickloman)
See the code for CONCOCT here: https://github.com/binpro/concoct