The Singular Demultiplex software can autodetect the FASTQ files from the folder path and file name prefix rather than requiring specifying each FASTQ file individually. In this case, the FASTQ input argument becomes --fastqs <folder>/<prefix>. The autodetection expects the following file structure, which is the standard G4 Sequencing Platform unfiltered_fastq output directory.

<folder>/<prefix>_L001_I1_001.fastq.gz
<folder>/<prefix>_L001_I2_001.fastq.gz
<folder>/<prefix>_L001_R1_001.fastq.gz
<folder>/<prefix>_L001_R1_001.fastq.gz
<folder>/<prefix>_L002_I1_001.fastq.gz
<folder>/<prefix>_L002_I2_001.fastq.gz
<folder>/<prefix>_L002_R1_001.fastq.gz
<folder>/<prefix>_L002_R1_001.fastq.gz
...

The autodetection will assume that files with _I1_ and _I2_ in the file name are index reads and that files with _R1_ and _R2_ in the file name are insert reads. The corresponding read structure for index reads will be +B while the corresponding read structure for insert reads will the +T. For the above example, the assumed read structure would be +B +B +T +T. You can specify an alternative reads structure via the --read-structures argument. The read structure arguments will be matched to the files via lexicographic order (i.e. I1, I2, R1, R2). The Singular Genomics Demultiplex program expects all FASTQ files in the folder to share the same read structure.

The autodetection feature also detects the different lanes via the _L00*_ portion of the file name. The default behavior of the Singular Genomics Demultiplex autodetection feature is to combine the demultiplexed output for each lane into a single set of FASTQ output files. Individual lanes can be demultiplexed using the --lane # option where # is the lane number to be demultiplexed. For onboard G4 Sequencing Platform demultiplexing, samples are demultiplexed at the lane level separately for each of the 4 lanes.