BCL To FASTQ

Use this skill when the input is an Illumina BCL run folder or the user asks to demultiplex a sequencing run. This is a deep demultiplexing and run-validation skill, not only a command wrapper.

Essential Inputs

Confirm:

• run folder path with RunInfo.xml
• sample sheet path and format
• output directory
• instrument/run metadata from RunInfo.xml and RunParameters.xml
• lane handling: split by lane or combine lanes
• index mismatch tolerance
• index read structure and dual-index orientation
• UMI layout, if any
• whether adapter trimming/masking should happen during conversion
• whether undetermined reads and demultiplexing metrics should be reviewed before downstream analysis