The corresponding command line option is the long name with the leading -- removed. For example, --filter-control-reads on the command line becomes filter-control-reads in the [Demux] section. When the command line option has an argument, the argument is entered in the next cell in the same row. When the option is specified both in the sample sheet and via the command line, the sample sheet parameters take precedence.

For example, instead of including both --filter-control-reads and --quality-mask-threshold 0 in the command line, we can include the following [Demux] section in the sample sheet instead.

[Demux]

filter-control-reads

quality-mask-threshold

0

For the standalone Singular Genomics Demultiplex software, all command line arguments can be used via the [Demux] section. For the onboard G4 Sequencing Platform demultiplex, only some options are supported.