yanlinlin82@gmail.com Linlin Yan sci-biology@gentoo.org Gentoo Biology Project 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: (1) Bisulfite mapping and methylation calling in one single step; (2) Supports single-end and paired-end read alignments; (3) Supports ungapped and gapped alignments; (4) Alignment seed length, number of mismatches etc. are adjustable; (5) Output discriminates between cytosine methylation in CpG, CHG and CHH context.