GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and
GSNAP: Genomic Short-read Nucleotide Alignment Program

Links are provided below in parentheses for users who wish to download the files with a command-line tool, like wget.


Source code for both GMAP and GSNAP

Release notices and bug reports

The old listserver mailing list is no longer being supported by EBI. The new mailing list for issues relating to both GMAP and GSNAP is now at Google Groups. To sign up, go to your list, select "All groups and messages", and search for "gsnap-users". Click on that group, and then "Join group". You can join there to receive release notices, ask questions, or see previous messages. If you have a bug to report or a feature to request, I believe you can also send email to gsnap-users@googlegroups.com. (You may have to subscribe to the list first, though, or the message will be held for me to approve) or directly to me at Thomas Wu (twu@gene.com).

Genome databases

You can build your own genome database with the gmap_build program included with this software. Please see instructions in the README file. For the human genome, you may want to retrieve


Documentation

README file from the source code distribution. Contains basic usage information.

Software demonstration given at ISMB 2005. Contains various examples of GMAP usage. [Slides]

References:

Thomas D. Wu and Colin K. Watanabe
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
Bioinformatics 2005 21:1859-1875 [Abstract] [Full Text]
Thomas D. Wu and Serban Nacu
Fast and SNP-tolerant detection of complex variants and splicing in short reads
Bioinformatics 2010 26:873-881
[Abstract] [Full Text]

Supplementary information for Bioinformatics 2005 publication on GMAP:


Thomas Wu
Last modified: Tue Aug 16 07:49:00 PDT 2011