--num-threads

Spawn a threadpool of N woker threads. The default is 0, meaning all available cores in the system.

--chunk-size

By default, each thread consumes N ZMWs per chunk for processing. The default is 10.

--no-bam

Do not produce BAM output, nor PBI. Useful if only the reports are of interest, as time to results is lower.

--no-reports

Do not produce any reports. Useful if only the demultiplexed BAM is of interest.

--keep-idx-order

Per default, the two identified barcode idx are sorted ascending, as in CLR data, the correct order cannot be determined. This affects the bc tag, prefix.counts file, and --split-bam file names; prefix.report columns IdxLowest, IdxHighest, IdxLowestNamed, IdxHighestNamed will have the same order as IdxFirst and IdxCombined. This option only makes sense for single read data, such as CCS.

If you are using an asymmetric barcode design with NxN pairs and your input is CCS, you can use --keep-idx-order to preserve the order. If your input is CLR subreads and you use NxN asymmetric pairs, there is no way to distinguish between pairs bc1001--bc1002 and bc1002--bc1001.