In Torrent Suite™ Software, the goal is to provide you with a view on alignment that helps determine run and library quality.

There are many alignment algorithms available in the marketplace and you are encouraged to consult with a bioinformatician for the most appropriate alignment algorithm for your downstream analysis needs. Alignment algorithms are also embedded in many commercial software tools available in the Ion Torrent™ Web store. You are also encouraged to experiment with these tools.

Alignment in Torrent Suite™ Software is performed using TMAP. TMAP is currently an unpublished alignment algorithm, created by the authors of the BFAST algorithm. Contact your Ion Torrent™ representative or Technical Support for more information on TMAP.

Although TMAP is unpublished and a reference is not currently available, the precursor to TMAP, BFAST, is based on the ideas in the following publications:

Homer N, Merriman B, Nelson SF.BFAST: An alignment tool for large-scale genome resequencing. PMID: 19907642PLoS ONE. 2009 4(11): e7767. http://dx.doi.org/10.1371/journal.pone.0007767

Homer N, Merriman B, Nelson SF. Local alignment of two-base encoded DNA sequence. BMC Bioinformatics. 2009 Jun 9;10(1):175.PMID: 19508732. http://dx.doi.org/10.1186/1471-2105-10-175