Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

Bioinformatics. 2011 Jun 1;27(11):1571-2. doi: 10.1093/bioinformatics/btr167. Epub 2011 Apr 14.


Summary: A combination of bisulfite treatment of DNA and high-throughput sequencing (BS-Seq) can capture a snapshot of a cell's epigenomic state by revealing its genome-wide cytosine methylation at single base resolution. Bismark is a flexible tool for the time-efficient analysis of BS-Seq data which performs both read mapping and methylation calling in a single convenient step. Its output discriminates between cytosines in CpG, CHG and CHH context and enables bench scientists to visualize and interpret their methylation data soon after the sequencing run is completed.

Availability and implementation: Bismark is released under the GNU GPLv3+ licence. The source code is freely available from

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cytosine / metabolism
  • DNA / chemistry
  • DNA Methylation*
  • Sequence Analysis, DNA*
  • Software*
  • Sulfites*


  • Sulfites
  • Cytosine
  • DNA
  • hydrogen sulfite