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,CHGandCHH*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 available in the PATH:
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 Publication
- Our review about primary data analysis in BS-Seq
- Our protocol "Quality Control, trimming and alignment of Bisulfite-Seq data"
Bismark was written by Felix Krueger, part of the Babraham Bioinformatics group.
Even though Bismark itself is a free software I would like to emphasize that the scripts bismark2report and bismark2summary produce HTML graphs using Highcharts. Highsoft software products (including Highcharts) are free to use for non-profit or academic use, but are are not free for commercial and Governmental use. For further information on Highsoft licensing please see here: www.highcharts.com.