Manual Installation

The conda installation should be enough for most users. However, if you want to modify the source code, a manual installation might be needed. An example of a manual installation on an Ubuntu system can be seen in the Travis CI config file.

Using Docker

We provide a Docker image: binpro/concoct_latest which contains CONCOCT and its dependencies for a basic workflow.

Assuming DOcker is installed, the following command will then download the image from the Docker image index, map the Data folder to the image and log you into the docker image.

docker run -v /home/USER/Data:/opt/Data -i -t binpro/concoct_latest bash

To test concoct you can then do:

$ cd /opt/CONCOCT_latest
$ nosetests

Which should execute all tests without errors.

Other Programs Needed

  • For assembly, use your favourite. Here is a good one:
  • To create the input bam files, choose your favourite aligner, for example bowtie2 or bwa.
  • For validation of clustering using single-copy core genes we recommend using: