Alignment

Torrent Suite™ Software provides a view on alignment that helps determine run and library quality.

Many alignment algorithms are available in the marketplace. You are encouraged to consult with a bioinformatician for the most appropriate alignment algorithm for your downstream analysis requirements.

Alignment in Torrent Suite™ Software is performed using TMAP. TMAP is currently an unpublished alignment algorithm, created by the authors of the BFAST algorithm. For more information, see TMAP modules, or contact your local Field Service Engineer or Technical Support.

Although TMAP is unpublished and a reference is not currently available, the precursor to TMAP, BFAST, is based on the ideas in the following publications: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 (2009) BFAST: An Alignment Tool for Large Scale Genome Resequencing. PLoS ONE 4(11): e7767. doi: 10.1371/journal.pone.0007767

• Homer N, Merriman B, Nelson SF (2009) Local alignment of two-base encoded DNA sequence. BMC Bioinformatics 10: 175. doi: 10.1186/1471-2105-10-175