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seqmap website  

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.

Environment Modules

Run module spider seqmap to find out what environment modules are available for this application.

System Variables

  • HPC_SEQMAP_DIR - installation directory
  • HPC_SEQMAP_BIN - executable directory
  • HPC_SEQMAP_DOC - documentation directory


If you publish research that uses seqmap you have to cite it as follows:

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