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Bismark

Function A tool to map bisulfite converted sequence reads and determine cytosine methylation states
Language Perl
Requirements A functional version of Bowtie or Bowtie2 is required. For BAM output Samtools is also required
Code Maturity Stable (for Bowtie and Bowtie2)
Code Released Yes, under GNU GPL v3 or later.
Mission Statement The less the people know about how sausages and our code are made, the better they sleep at night (untracable author)
Initial Contact Felix Krueger

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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:

This link will take you to the Bismark publication.

This link will take you to our review about primary data analysis in BS-Seq.

This link will take you to our protocol 'Quality Control, trimming and alignment of Bisulfite-Seq data' at the Epigenesys website.

Here you can access the Bismark documentation Bismark User Guide (pdf).

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

Changelog