GSNAP
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Application data |
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| Biological application domain(s) | RNA-Seq alignment, DNA methylation |
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| Principal bioinformatics method(s) | Read mapping, Bisulfite mapping |
| Created at | Genentech |
| Maintained? | Maybe |
| Programming language(s) | C, Perl |
Summary: GSNAP can align both single-end and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite treated DNA for the study of methylation state.
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Limitations
- Does not seem to support color space.
Links
References
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