CONCOCT - Clustering cONtigs with COverage and ComposiTion
Intro
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/Documentation
For the most comprehensive information about the usage and function of CONCOCT so far, see the complete example.
Installation
For up to date instructions for installation, see github.
Credits
The logo is a derivative from an original by Norma Umer.
Contributors
Dr Christopher Quince (chrisquince)
Johannes Alneberg (alneberg)
Brynjar Smari Bjarnasson (binnisb)
Ino de Bruijn (inodb)
Dr Umer Zeeshan Ijaz (umerijaz)
Dr Nick Loman (nickloman)
Licence
FreeBSD
See the code for CONCOCT here: https://github.com/binpro/concoct
