spliced and SNP-tolerant alignment for mRNA and short reads


This package contains the programs GMAP and GSNAP as well as utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning EST, mRNA and cDNA sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single-end and paired-end transcriptome reads. Both tools can use a database of
 * known splice sites and identify novel splice sites.
 * known single-nucleotide polymorphisms (SNPs).
GSNAP can align bisulfite-treated DNA.

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