Genome binning with CONCOCT
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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:

   https://github.com/BinPro/CONCOCT/

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