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.

Documentation

• Bismark home
• Publication: Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications Bioinformatics. 2011 Jun 1;27(11):1571-2. doi: 10.1093/bioinformatics/btr167

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