FASTQ Files Directory
The software writes compressed, demultiplexed FASTQ files to folders named to corresponding samples listed in the sample sheet.
If a sample sheet includes multiple samples per lane, the indexes must be specified. If they are not specified, the software displays a missing barcode error and ends the analysis.
The software allows one unindexed sample because identification is not necessary to sequence one sample. However, sequencing multiple samples requires multiplexing so the samples can be identified for analysis.