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Bismark

Description

bismark website

Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. It's main features are:

  • Bisulfite mapping and methylation calling in one single step * Supports single-end and paired-end read alignments * Supports ungapped and gapped alignments * Alignment seed length, number of mismatches etc. are adjustable * Output discriminates between cytosine methylation in CpG, CHG and CHH context

Environment Modules

Run module spider bismark to find out what environment modules are available for this application.

Environment Variables

  • HPC_BISMARK_DIR - installation directory
  • HPC_BISMARK_BIN - executable directory
  • HPC_BISMARK_DOC - documentation directory

Citation

If you publish research that uses bismark you have to cite it as follows:

Krueger, F., & Andrews, S. R. (2011). Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27(11), 1571–1572. https://doi.org/10.1093/bioinformatics/btr167

Categories

biology, ngs