Upload a new reference file
As part of the standard analysis process, reads are aligned to a genomic reference, using the TMAP aligner that comes pre-installed on the Torrent Server.
Note:
Currently, the variantCaller plugin does not support IUPAC base codes other than A, C, T, G, and N. When Torrent Suite™ software uploads a genome containing other IUPAC characters, each such character is replaced with N.
For a new genome sequence, use the tab to add the new reference genome. (These reference sequences are also displayed on the Ion PGM™ or Ion Proton™ Sequencer when you load a sample.)