Bismark

Application data
Created by	Felix Krueger
Biological application domain(s)	Epigenomics, Genomics
Principal bioinformatics method(s)	Bisulfite Mapping, Mapping, Methylation Calling
Technology	independent, but developed for Illumina files
Created at	The Babraham Institute, Babraham Bioinformatics
Maintained?	Yes
Input format(s)	FASTQ, FASTA
Output format(s)	custom Bismark output format
Software features	fast and convenient Bisulfite-Seq output, very flexible
Programming language(s)	Perl
Licence	GPLv3
Operating system(s)	Linux

Summary: Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.

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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 IIx, while retaining much of the flexibility of Bowtie (adjust the seed length, number of mismatches, --best...). 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.

Links

• Bismark Homepage [ edit link ]
• Bismark Homepage [ edit link ]

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www.bioinformatics.bbsrc.ac.uk/projects/

References

1. . 2011. Bioinformatics

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