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Bismark

A software package to map and determine the methylation state of BS-Seq reads. Bismark is easy to use, very flexible and is the first published BS-Seq aligner to seamlessly handle single- and paired-end mapping of both directional and non-directional bisulfite libraries. The output of Bismark is easy to interpret and is intended to be analysed directly by the researcher performing the experiment.

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1 user review

1 user review

Shaojun Xie's avatar image Shaojun Xie's country flag

Shaojun Xie

Bismark is a great tool for the alignment of BS-seq reads.

Bismark forum

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Bismark versioning

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Bismark classification

Bismark specifications

Software type:
Package/Module
Restrictions to use:
None
Output format:
SAM, tab-delimited text
Programming languages:
Perl
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Conda:
https://bioconda.github.io/recipes/bismark/README.html
Interface:
Command line interface
Input format:
FASTQ
Operating system:
Unix/Linux
License:
GNU General Public License version 2.0
Version:
0.14.3
Requirements:
Bowtie/Bowtie2
Galaxy:
https://toolshed.g2.bx.psu.edu/repository?repository_id=0df2df1072d600d7

Bismark support

Maintainer

  • Felix Krueger <>

Credits

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Publications

Institution(s)

Bioinformatics Group, The Babraham Institute, Cambridge, UK

Funding source(s)

Biotechnology and Biological Sciences Research Council (BBSRC)

Link to literature

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