Omixon release a very fast and very sensitive mapping tool for letter space data.
The range of Omixon products has been expanded with the addition of a new command line toolkit, called the Letter Space Toolkit. This contains a tool called ORM which is a letter space mapping and alignment tool. It is both very fast and very precise has a number of unique features including variable density indexing for exome and other targetted sequencing, mapping of long indels, handling of tandem repeats and more.
ORM will align data from the Illumina, Ion Torrent and Roche 454 platforms. This first version is a beta release.