Spawn a threadpool of
N woker threads. The default is
0, meaning all available cores in the system.
By default, each thread consumes
N ZMWs per chunk for processing. The default is
Do not produce BAM output, nor PBI. Useful if only the reports are of interest, as time to results is lower.
Do not produce any reports. Useful if only the demultiplexed BAM is of interest.
Per default, the two identified barcode idx are sorted ascending, as in CLR data, the correct order cannot be determined. This affects the
prefix.counts file, and
--split-bam file names;
IdxHighestNamed will have the same order as
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