--use-bases-mask is not longer a command line option. Overriding cycles can be indicated in the samplesheet using OverrideCycles,Y#;N#. If using a standard dual index length 10 (padded or not) samplesheet for a NovaSeq flowcell, no --use-bases-mask or OverrideCycles,Y#;N# is needed.
The option --barcode-mismatches is removed and needs to be indicated in the samplesheet by using BarcodeMismatchIndex1,#, and BarcodeMismatchIndex2,#.
bcl2fastq -> BCL Convert quick guide: https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html
current bcl2fastq command for NovaSeq:
Converted BCL Convert command:
Notes:
--use-bases-mask
is not longer a command line option. Overriding cycles can be indicated in the samplesheet usingOverrideCycles,Y#;N#
. If using a standard dual index length 10 (padded or not) samplesheet for a NovaSeq flowcell, no--use-bases-mask
orOverrideCycles,Y#;N#
is needed.--barcode-mismatches
is removed and needs to be indicated in the samplesheet by usingBarcodeMismatchIndex1,#
, andBarcodeMismatchIndex2,#
.DRAGEN Overview: https://emea.support.illumina.com/content/dam/illumina-marketing/documents/products/technotes/dragen-integration-tech-note-970-2020-006.pdf
DRAGEN USer Guide: https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/dragen-bio-it/dragen-bio-it-platform-v3.6-user-guide-1000000128306-00.pdf