Command Line Args (Advanced) screen

When planning a Sample Set in the Barcoding step in the workflow bar, you can click Custom, then use the Advanced Options screen to customize advanced arguments for analysis parameters.

Argument	Description
Beadfind args	Beadfind module command line arguments. These arguments should not be modified unless instructed by Ion Torrent™ Technical Support.
Analysis args	Analysis command line arguments. These arguments should not be modified unless instructed by Ion Torrent™ Technical Support.
Pre Basecaller args for calibration	BaseCaller command line arguments. For information on `--barcode-mode`, `--barcode-cutoff`, and `--barcode-filter` parameters, see BaseCaller module arguments. This field is used only if a Base Calibration Mode other than 'No Calibration' is used. Other BaseCaller arguments should not be modified unless instructed by Ion Torrent™ Technical Support.
Recalibration Args	Recalibration command line arguments.
Basecaller Args	BaseCaller command line arguments. For information on `--barcode-mode`, `--barcode-cutoff`, and `--barcode-filter`, see BaseCaller module arguments. Other BaseCaller arguments should not be modified unless instructed by Ion Torrent™ Technical Support.
Alignment Args	Arguments for the TMAP aligner. This replaces the TMAP Args setting that appears in previous software releases.