libyarlaylab/bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

Bismark

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, CHG and CHH * context

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).