GSNAP

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Application data

Biological application domain(s) RNA-Seq alignment, DNA methylation
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

  1. . 2010. Bioinformatics


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