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{{Bioinformatics application
|sw summary=Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
|bio domain=Epigenomics, Genomics, DNA methylation|bio method=Bisulfite Mappingmapping, MappingRead mapping, Methylation Calling|bio tech=independent, but developed for Illumina filescalling
|created by=Felix Krueger
|created at=The Babraham Institute, Babraham Bioinformatics
|maintained=Yes
|input format=FASTQ, FASTA
|output format=SAM (or custom Bismark output format)
|sw feature=fast and convenient Bisulfite-Seq output, very flexible
|language=Perl
|licence=GPLv3, |os=Linux, Mac OS X, Windows
}}
Bismark supports both single-end and paired-end read mapping of Bisulfite-Seq data in either fastA or fastQ format produced by e.g. the Illumina Genome Analyser IIxplatform, while retaining much of the flexibility of Bowtie (adjust the seed length, number of mismatches, --best, insert sizes ...). Sequence reads are first transformed into fully bisulfite-converted forward (C > T) and reverse reads (G > A conversion of the forward strand), before aligning them to similarly converted versions of the genome (also C>T and G>A). Sequence reads that produce a unique best alignment from the four alignment processes against the bisulfite genome (which are running in parallel), are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is determined.
As of version 0.6.x Bismark does also support gapped alignments using Bowtie 2.
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