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Fix for "C methylated in Unknown context..." in PE alignment and bismark2report alignment report processing

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Build Status install with bioconda


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, gapped or spliced alignments
  • Alignment seed length, number of mismatches etc. are adjustable
  • Output discriminates between cytosine methylation in CpG, CHG and CHH context


Bismark is written in Perl and is executed from the command line. To install Bismark simply download the latest release of the code from the Releases page and extract the files into a Bismark installation folder.

Bismark needs the following tools to be installed and ideally available in the PATH environment:


The Bismark documentation can be found with the code in the Docs subfolder and also read online.

There is also an overview of the alignment modes that are currently supported by Bismark: Bismark alignment modes (pdf).



Bismark was written by Felix Krueger, part of the Babraham Bioinformatics group.


Bismark itself is free software, bismark2report and bismark2summary produce HTML graphs powered by which are also free to use and look at!