Novaseq demultiplexing on Dragen

[barrystokman]

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:

bcl2fastq --loading-threads 3 --processing-threads 15 --writing-threads 3 --runfolder-dir ${RUN_DIR} --output-dir ${DEMUX_DIR}/${UNALIGNED_DIR} --use-bases-mask ${BASEMASK} --sample-sheet ${RUN_DIR}/SampleSheet.csv --barcode-mismatches 1

Converted BCL Convert command:

bcl-convert  --bcl-input-directory  ${RUN_DIR}  --output-directory ${DEMUX_DIR}/${UNALIGNED_DIR} --sample-sheet ${RUN_DIR}/SampleSheet.csv

Notes:

1. --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.
2. The option --barcode-mismatches is removed and needs to be indicated in the samplesheet by using BarcodeMismatchIndex1,#, and BarcodeMismatchIndex2,#.

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

[henrikstranneheim]

@barrystokman Done?

[barrystokman]

yes, closing