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https://github.com/FelixKrueger/Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states
https://github.com/FelixKrueger/Bismark

bioinformatics dna methylation

Last synced: about 2 months ago
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A tool to map bisulfite converted sequence reads and determine cytosine methylation states

Host: GitHub
URL: https://github.com/FelixKrueger/Bismark
Owner: FelixKrueger
License: gpl-3.0
Created: 2015-11-07T18:14:13.000Z (almost 9 years ago)
Default Branch: master
Last Pushed: 2024-07-31T09:04:42.000Z (about 2 months ago)
Last Synced: 2024-07-31T10:24:36.606Z (about 2 months ago)
Topics: bioinformatics, dna, methylation
Language: HTML
Homepage: http://felixkrueger.github.io/Bismark/
Size: 38.1 MB
Stars: 370
Watchers: 15
Forks: 99
Open Issues: 22
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: license.txt

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README

# Bismark

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bismark/README.html)

> **See the documentation**:

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](http://www.bioinformatics.babraham.ac.uk/projects/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, gapped or spliced alignments
- Alignment seed length, number of mismatches etc. are adjustable
- Output discriminates between cytosine methylation in `CpG`, `CHG` and `CHH` context

## Documentation

The Bismark documentation can be found with the code in the [docs](docs) subfolder and can also be read online:

There is also an overview of the alignment modes that are currently supported by Bismark: [Bismark alignment modes](http://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_alignment_modes.pdf) (pdf).

## Installation

Bismark is written in Perl and is executed from the command line. To install Bismark simply download the latest release of the code from the [Releases page](https://github.com/FelixKrueger/Bismark/releases) and extract the files into a Bismark installation folder.

Bismark needs the following tools to be installed and ideally available in the `PATH` environment:

- [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/) or [HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml) or [minimap2](https://lh3.github.io/minimap2/minimap2.html)
- [Samtools](http://www.htslib.org/)

## Links

- Bismark Publication
- http://www.ncbi.nlm.nih.gov/pubmed/21493656
- Our review about primary data analysis in BS-Seq
- http://www.ncbi.nlm.nih.gov/pubmed/22290186

## Credits

Bismark was written by Felix Krueger, part of the [Babraham Bioinformatics](http://www.bioinformatics.babraham.ac.uk/projects/bismark/) group.

## Licences

Bismark itself is free software, `bismark2report` and `bismark2summary` produce HTML graphs powered by [Plot.ly](https://plot.ly/javascript/) which are also free to use and look at!