Difference between revisions of "Bismark"
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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), | 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. | 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. | ||
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Revision as of 14:12, 14 June 2010
Application data |
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Created by | Felix Krueger |
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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
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 |
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