Question: What do I need to demultiplex NovaSeq data?
Answer: bcl2fastq 2.19 was the first version to support the CBCL files produced by the Novaseq, as opposed to the traditional BCL files. It supported the original S2 flowcell. bcl2fastq 2.20 is a required update that supports the S4 flow cell. Cell Ranger 2.1 fully supports RTA 3.3, and both S2 and S4 on NovaSeq.