Notes about the --barcode-cutoff parameter with --barcode-mode 1:

• 0 is the most restrictive setting. --barcode-cutoff 0 allows only reads that perfectly match a barcode in base space.

• The setting 0 works with any barcode set (both Ion Torrent™ sets and custom barcode sets).

• Do not set --barcode-cutoff greater than 2 with the IonXpress barcode set. Values greater than 2 relax the classification rules and allow incorrect barcode assignments.

A rule of thumb for the maximum --barcode-cutoff setting is based on the minimum distance of the barcode set in flow space:

T he minimum distance for the IonXpress barcode set is 5. Then the maximum recommended value for --barcode-cutoff is 2 for analyses that use the IonXpress barcode set.