Bismarkis a program to align bisulfite treated sequencing reads (BS-Seq) to a reference genome and perform methylation calls for every cytosine in the read in a single step. The output can be easily imported into a genome viewer such as SeqMonk, enabling researchers to analyse their data straight away.
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Bioinformatics. 2011 Jun 1;27(11):1571-2. Epub 2011 Apr 14.
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.
Krueger F, Andrews SR.