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

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

Shaojun Xie

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

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Bismark classification

Bismark specifications

Software type:
Package
Restrictions to use:
None
Output format:
SAM, tab-delimited text
Programming languages:
Perl
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Input format:
FASTQ
Operating system:
Unix/Linux
License:
GNU General Public License version 2.0
Version:
Bismark version 0.14.3
Requirements:
Bowtie/Bowtie2

Publications

  • (Krueger and Andrews, 2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics.
    Published on: 2011 Jun 01
    PMID: 21493656

Bismark support

Maintainer

Credits

Institution(s)

Bioinformatics Group, The Babraham Institute, CB22 3AT, Cambridge, UK

Funding source(s)

Biotechnology and Biological Sciences Research Council (BBSRC)

Link to literature

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