The Command Line Args (Advanced) tab

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