Difference between revisions of "Bismark"
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{{Bioinformatics application | {{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. | |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 | + | |bio domain=Epigenomics, Genomics, DNA methylation |
| − | |bio method=Bisulfite mapping, | + | |bio method=Bisulfite mapping, Read mapping, Methylation calling |
|created by=Felix Krueger | |created by=Felix Krueger | ||
|created at=The Babraham Institute, Babraham Bioinformatics | |created at=The Babraham Institute, Babraham Bioinformatics | ||
|maintained=Yes | |maintained=Yes | ||
|input format=FASTQ, FASTA | |input format=FASTQ, FASTA | ||
| − | |output format=custom | + | |output format=SAM (or custom) |
|sw feature=fast and convenient Bisulfite-Seq output, very flexible | |sw feature=fast and convenient Bisulfite-Seq output, very flexible | ||
|language=Perl | |language=Perl | ||
|licence=GPLv3, | |licence=GPLv3, | ||
| − | |os=Linux | + | |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 | + | 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. | + | 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}} | {{Links}} | ||
{{References}} | {{References}} | ||
{{Link box}} | {{Link box}} | ||
Latest revision as of 18:32, 5 November 2015
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Application data |
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| Created by | Felix Krueger |
|---|---|
| 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.
"Error: no local variable "counter" was set." is not a number.
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
To add a reference for Bismark, enter the PubMed ID in the field below and click 'Add'.
Search for "Bismark" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
