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Genome binning with CONCOCT

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:

  • Generate a co-assembly from all the reads in your dataset (or a subset if too large)
  • Map reads back on a per-sample basis to the contigs to generate coverage information
  • Run CONCOCT to produce clusters
  • (optionally) Link clusters with paired-end reads
  • Evaluate results, e.g. using taxonomic assignments of contigs and presence of conserved genes in clusters

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:

http://www.youtube.com/watch?v=tSul_qDwvN4&t=1h15m32s

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LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.

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.

© Copyright 2013, Holly Bik, C. Titus Brown, Nick Loman, Lex Nederbragt, Jared Simpson. Created using Sphinx 1.1.3.

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