Bismark
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Application data |
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| Created by | Felix Krueger |
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| Biological application domain(s) | Epigenomics, Genomics, DNA methylation |
| Principal bioinformatics method(s) | Bisulfite mapping, Read mapping, Methylation calling |
| Created at | The Babraham Institute, Babraham Bioinformatics |
| Maintained? | Yes |
| Input format(s) | FASTQ, FASTA |
| Output format(s) | SAM (or custom) |
| Software features | fast and convenient Bisulfite-Seq output, very flexible |
| Programming language(s) | Perl |
| Licence | GPLv3 |
| Operating system(s) | Linux, Mac OS X, Windows |
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 platform, 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.
Links
References
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