Cutoff setting

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

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

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

• Do not set --barcode-cutoff greater than 2 with the Ion Xpress™ Barcode Adapters 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:

The minimum distance for the Ion Xpress™ Barcode Adapters barcode set is 5. The maximum recommended value for --barcode-cutoff is 2 for analyses that use the Ion Xpress™ Barcode Adapters barcode set.