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Bismark

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General Description

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

Basic Usage

module load bio/bismark

Useful Options


Further Information

See the official website: Babraham Bioinformatics