Bismark 0.16.3

Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.

Accessing the software

There are 2 modules available for this version of Bismark. One with Bowtie 1.0 and one with Bowtie 2.1.0. Load the one that is relevant for your needs:

$ module load apps/bismark/v0.16.3_bowtie1
$ module load apps/bismark/v0.16.3_bowtie2

To view command-line options, run the following command:

$ bismark --help

Some additional, useful environment variables that are set when loading Bismark:

  • BISMARK_UG refers to the User Guide in psf format.
  • BISMARK_RRBS_GUIDE refers to the RRBS Guide in pdf format.

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

Previous versions of this application are recorded below:

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the Bismark Github repository for more information regarding this application.

Last modified: 12 October 2017