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: 22 days 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 (over 9 years ago)
- Default Branch: master
- Last Pushed: 2025-01-06T07:26:59.000Z (4 months ago)
- Last Synced: 2025-01-06T08:29:05.016Z (4 months ago)
- Topics: bioinformatics, dna, methylation
- Language: HTML
- Homepage: http://felixkrueger.github.io/Bismark/
- Size: 38.1 MB
- Stars: 402
- Watchers: 14
- Forks: 104
- Open Issues: 28
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Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: license.txt
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README
# Bismark
[](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!