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See the documentation:https://felixkrueger.github.io/Bismark

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 asSeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. Its 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 inCpG,CHG andCHH context

The Bismark documentation can be found with the code in thedocs subfolder and can also be read online:https://felixkrueger.github.io/Bismark/

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

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

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

• Bowtie2 orHISAT2 orminimap2
• Samtools

• Bismark Publication:http://www.ncbi.nlm.nih.gov/pubmed/21493656
• Our review about primary data analysis in BS-Seq:http://www.ncbi.nlm.nih.gov/pubmed/22290186

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

Bismark itself is free software,bismark2report andbismark2summary produce HTML graphs powered byPlot.ly which are also free to use and look at!