CONCOCT is automated genome binning software that can use coverage information across multiple samples, composition and paired-end linkage information.
The manuscript describing the software is available on arXiv:
CONCOCT: Clustering cONtigs on COverage and ComposiTion http://arxiv.org/abs/1312.4038
The Github repository is here:
The basic steps are as follows:
To install CONCOCT, follow the instructions here:
https://github.com/BinPro/CONCOCT
A complete walk-through is available here:
https://github.com/BinPro/CONCOCT/blob/master/doc/complete_example.md
A repository containing the input and output files for a simple, worked example is available here:
https://github.com/BinPro/CONCOCT-test-data
A recent presentation by Chris Quince on CONCOCT is available to “watch again” from Beatles and Bioinformatics at this link:
Development and posting of this material, and the associated workshop, were supported by Grant Number R25HG006243 from the National Human Genome Research Institute and an NSF OCI supplement to NSF DBI-0939454.
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