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.
- 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
To see what versions of Bismark are available type
module avail bismark
To see what other modules are needed, what commands are available and how to get additional help type
module help bismark
To use Bismark, include a command like this in your batch script or interactive session to load the Bismark module:
module load bismark
Be sure you also load any other modules needed, as listed by the
module help bismark command.