NovaSeq 6000 File-based v2.3.0

The NovaSeq 6000 Integration v2.3 has the following compatibility:

• Clarity LIMS v4.2 or later, until v6.0. Not compatible with v6.0 or later.

• NGS Extensions Package v5.20 or later.

• NovaSeq Control Software (NVCS) v1.7.0.

• Illumina Bcl2FastQ v2.20.

Features to Note for this Release

This release of Clarity LIMS integration package provides:

• Support for the NovaSeq Control Software v1.7.0 with v1.5 reagents.

• Support for asymmetric sequencing read length.

• Support for reverse complement workflow in sample sheet generation.

• Support for Unique Molecular Identifiers (UMI) configuration that is populated in sample sheet.

• Updated preconfigured workflow (NovaSeq 6000 v2.1).

• Support SPrime (SP) flow cell in the preconfigured workflow.

• PhiX spike-in volume calculation script.

• Update to the latest flow cell barcode mask.

• New secret management mechanism.

Defects Fixed

• Fixed the 'NULL' value for custom primer settings in JSON recipe issue.

• Fixed the lane number discrepancy issue in Automated - NovaSeq Run step.

Known Issues

Minor bug in SecretUtil v1.0.0 that causes some NGS automation scripts to fail if the command does not have -l parameter. This will be fixed in the SecretUtil v1.0.1 release (Dec 2020). Until then, add "-l" in the automation script to bypass the bug i.e. bash -l -c "......". The automation scripts affected are:

• assignQC

• assignQCForDemuxStep

• parseBioAnalyzer

• parseCSV

• place_samples_by_robot_file

• parseXmlBySampleName