GSNAP

Application data
Biological application domain(s)	RNA-Seq, DNA Methylation
Principal bioinformatics method(s)	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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