Home 9 Resources 9 Software 9 BISMARK


Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.

Bismark requires Bowtie or Bowtie2. For BAM output, SAMtools is required.


Usage on Bridges-2

To see what versions of Bismark are available and if there is more than one, which is the default, along with some help, type

module spider bismark

To use Bismark, include a command like this in your batch script or interactive session to load the Bismark module: (note ‘module load’ is case-sensitive):

module load bismark