SeqMap - A Tool For Mapping Millions Of Short Sequences To The Genome

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(These are the major updates only, for all revisions, see HISTORY.txt)

Aug 20, 2008 - SeqMap 1.0.8 changed quite a lot to improve user experiences.

Aug 12, 2008 - The SeqMap paper has been accepted by Bioinformatics.

June 27, 2008 - Support reads longer than 32bp, and reads have letter N.

June 19, 2008 - Support Eland format output.

February 12, 2008 - HISTORY.txt file is done.

February 11, 2008 - SeqMap 1.0.0 is now online. Documatation and website are still under construction.


SeqMap is a tool for mapping large amount of oligonucleotide to the genome. It is designed for finding all the places in a genome where an oligonucleotide could potentially come from. SeqMap can efficiently map as many as dozens of millions of short sequences to a genome of several billions of nucleotides. While doing the mapping, several mutations as well as insertions/deletions of the nucleotide bases in the sequences can be tolerated and furthermore detected. Various input and output formats are supported, as well as many command line options for tuning almost every steps in the mapping process. A typical mapping can be done in a few hours on an ordinary PC.


SeqMap was started in the Wong Lab and is developed and maintained by Hui Jiang.


Jiang, H., Wong, W.H. (2008) SeqMap: Mapping Massive Amount of Oligonucleotides to the Genome, Bioinformatics, 24(20). [online]


Anyone can use the source codes, documents or the excutable file of SeqMap free of charge for non-commercial use. For commercial use, please contact the author.


1.0.13 source (for all platform)

1.0.12 32-bit (x86, Windows)
1.0.12 32-bit (x86, Linux)
1.0.12 64-bit (x86_64, Linux)
1.0.12 32-bit (ppc, Mac OS X)
1.0.12 64-bit (ppc_64, Mac OS X)

A sample C++ code for combining several output files generated by SeqMap in parallel in /output_statistics format.


(last modified on September 9, 2011 3:49 PM )