Aligns both single- and paired-end reads as short as 14 nt and of arbitrarily long length. GSNAP can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or a database of known splice sites. GSNAP 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.
Restrictions to use:
Command line interface
Fast and SNP-tolerant detection of complex variants and splicing in short reads. Published in: 2010 PMID: 20147302 DOI: 10.1093/bioinformatics/btq057