| | Path of Illumina BCL run folder. |
| | The path to the simple layout sample sheet. |
| | bcl2fastq option. Semicolon-delimited series of lanes to demultiplex. Use this if you have a sample sheet for an entire flow cell but only want to generate a few lanes for further 10x Genomics analysis. |
| | bcl2fastq option. Use to clip extra bases off a read if you ran extra cycles for QC. |
| | bcl2fastq option. Delete the Undetermined FASTQs generated by bcl2fastq. Useful if you are demultiplexing a small number of samples from a large flow cell. |
| | bcl2fastq option. Use this option to change the number of allowed mismatches per index adapter (0, 1, 2). |
| | The folder to store the demux results |