Bismark

Description

bismark website

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

Environment Modules

Run module spider bismark to find out what environment modules are available for this application.

Environment Variables

• HPC_BISMARK_DIR - installation directory
• HPC_BISMARK_BIN - executable directory
• HPC_BISMARK_DOC - documentation directory

Citation

If you publish research that uses bismark you have to cite it as follows:

Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011 Jun 1;27(11):1571-2. doi: 10.1093/bioinformatics/btr167. Epub 2011 Apr 14. PubMed PMID: 21493656; PubMed Central PMCID: PMC3102221.

Categories

biology, ngs