# 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