Beginning in Torrent Suite 4.4, there is a base calibration mode drop-down menu. For Torrent Suite™ Software v5.2, this menu contains four options: Default Calibration, Enable Calibration Standard, Blind Calibration, and No Calibration. (Previously, in Torrent Suite™ Software v4.2, you could choose to Enable Base Recalibration or not.) You can select the base calibration method during run planning and in the reanalysis menu.

Default Calibration – allows a random subset of wells to be used for base calibration. (This is equivalent to the default setting for Torrent Suite™ Software v4.2 and earlier, i.e., a checked Enable Base Recalibration check box). This option uses TMAP to align the training subset of wells and is recommended if a good reference for the template is available.

Blind Calibration – uses the same random subset of wells as Default Calibration but does not require an alignment step to generate the calibration model. This option is recommended if the template does not align well to a reference genome or if no reference is specified.

Enable Calibration Standard – allows wells belonging to the Calibration Standard to be selected as training subset.

The Calibration Standard is a small panel consisting of known sequence content with comprehensive and uniform representation of long homopolymers (up to 10-mers). The calibration standard can be spiked into Ion S5™, Ion PGM™, and Ion Proton™ runs as a quality control for higher homopolymer performance and as a known reference for base recalibration.

The Calibration Standard is designed for use in combination with IonXpress or IonCode barcoded libraries. The calibration standard sequences are around 200 base pairs in length. Dor best results, the DNA templates should have similar read lengths.

Please note that this method of base calibration only works if calibration standard beads were spiked into the run. A summary of the number of calibration standard beads found can be viewed under the Calibration Report tab on the run page.