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Function A tool to map bisulfite converted sequence reads and determine cytosine methylation states
Language Perl
Requirements A functional version of Bowtie2 or HISAT2 is required. For BAM output Samtools is also required
Code Maturity Stable
Code Released Yes, under GNU GPL v3 or later
Mission Statement The less 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:

Bismark is now also available from GitHub. You are invited to leave comments, feature request or bug reports over there!

This link will take you to the Bismark publication.

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

Here you can access the Bismark documentation Bismark User Guide.

Here are some sample Bismark HTML reports: paired-end BS-Seq processing report, or a single-end PBAT processing report

Or some Bismark HTML summary reports: Bismark Summary Report WGBS, Bismark Summary Report RRBS (no deduplication), or a Bismark Summary for a single-cell experiment which summarises a larger number of samples (Bismark Summary single cells data (.txt))

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