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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


  • Operation: Read mapping; Bisulfite mapping
  • Input: FASTQ; FASTA; .txt
  • Output: .txt; FASTQ
  • Software interface: Command-line user interface
  • Language: Perl;C
  • Operating system: Linux; Mac OS X
  • License: Other
  • Cost: Free
  • Version name: -
  • Credit: -
  • Contact: Thomas D. Wu twu _at_
  • Collection: -


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.
PMID: 20147302
PMCID: PMC2844994

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.
PMID: 27008021

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