--barcode-cutoff

1.0

(Float)

Maximum distance allowed in barcode matches. A threshold that sets the stringency for barcode matches. Lower values require more exact matches when assigning reads to barcodes. Higher values allow less exact matches.

Reads that have a distance greater than this value are counted as barcode no-matches.

--barcode-mode

2

(Integer)

Allowed values: 1, 2

• 1: A barcode is scored by comparing each read sequence to each barcode sequence in a flow space alignment. Errors in each flow are summed over the length of the barcode flows.Then any barcode with a number of errors equal to or less than the --barcode-cutoff value can be considered, and the barcode with the fewest errors with respect to the input sequence is the matching barcode.(The default in 4.0, known as hard decision classification.) 2: Barcode classification is based on signal information,specifically on the squared distance between the measured signal and the predicted barcode signal. (The default in 4.4, known as soft decision classification.)

--barcode-separation

2.5

( Float)

This setting controls how much ambiguity in barcode assignment you want to tolerate, by investigating the distances to the both the closest barcode and to the next closest barcode. A read is rejected if the difference in these two distances is less than the --barcode-separation setting.

--barcode-filter-postpone

1

Allowed values: 0, 1, 2

• 0: Keeps the 4.0 behavior: b arcode filtering is done independently on each block. This is the default for all Ion PGM™ analyses and also for Ion Proton™ thumbnail (which only consist of a single block) processing and base calibration training stage processing.

• 1: BaseCaller does barcode pre-filtering at a 10x lower frequency threshold (10 times more lenient). B arcode filtering is done on the chip's full information as a whole, after the 96 blocks are merged into one. This is the default for Ion Proton™ full-chip (not thumbnail) analyses.

• 2: The BaseCaller does not do any barcode pre-filtering. All barcode classification happens after the 96 blocks are merged into one. (The setting "2" is slower than the setting "1". "2" creates more files and involves more processing than "1".)

--barcode-filter

0.01

(Float)

Barcode frequency threshold to be reported in the UI. The relative frequency of a barcode is the number of assigned reads divided by number of reads assigned to the most frequent barcode.

Set to 0.0 to turn this filter off. The setting 0.0 causes all barcodes in the barcode set to be reported in the UI, including barcodes with no or very few reads, provided that the barcode group has at least --barcode-filter-minreads number of reads. (Typically barcodes with no or very few reads are not relevant to your analysis and should be filtered out.)

--barcode-filter-minreads

20

(INT)

Threshold for the minimum number of reads in a barcode group, for that group to be reported in the UI.

--trim-barcodes

on

Trim barcode and barcode adapter. If off, disables all other 5’ trimming.

--barcode-adpter-check

0.15

Validate barcode adapter sequence. The parameter given is the maximum allowed squared residual per flow. This feature reduces barcode set cross contamination, e.g., between the IonXpress and IonCode barcode sets. (0=off)