GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool to align single- and paired-end reads to a reference genome. The GSNAP algorithm is based on the seed-and-extend method and works on reads down to 14 nucleotides of length, and computes SNP-tolerant alignments of various combinations of major and minor alleles. The algorithm can discover long-distance and interchromosomal splicing events by utilizing known splice sites data or by probabilistic models. In addition, the GSNAP algorithm can construct alignments using reads originating from bisulfite-treated DNA samples.
Genomic; Epigenetics; RNA-seq
Wu TD, Nacu S "Fast and SNP-tolerant detection of complex variants and splicing in short reads." Bioinformatics. 2010 Apr 1;26(7):873-81. 2010 Feb 10. https://doi.org/10.1093/bioinformatics/btq057
Wu TD, Reeder J, Lawrence M, Becker G, Brauer MJ "GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and Functionality." Methods Mol Biol. 2016;1418:283-334. https://doi.org/10.1007/978-1-4939-3578-9_15
If you find errors, please report here.