# Release Notes

Last Updated: November 2024

Release Date: June 2024

Document Version: 2

These release notes describe the key changes to software components for the Clarity LIMS NextSeq 1000/2000 Integration Package v2.5.0.

## Compatibility

Refer to [Compatibility](https://help.connected.illumina.com/clarity-lims/compatibility#nextseq-1000-2000) under Instruments & Integrations.

## New Features

* Updates the Demultiplexing step in NextSeq 1000/2000 Sequencing workflow with the following changes:
  * The Sample Details table displays the index sequence.
  * The Sample Details table only displays the following demultiplexing stats due to changes in *Demultiplex\_Stats.csv*:
    * \# Reads
    * \# Perfect Index Reads
    * \# One Mismatch Index Reads
  * The demultiplexing stats displayed are aggregated for multi-lane flow cells (for example, P3).
  * The following run metrics files are included in *Run\_Metrics.zip* and attached to the step:
    * *Adapter\_Metrics.csv*
    * *Demultiplex\_Stats.csv*
    * *Index\_Hopping\_Counts.csv*
    * *Quality\_Metrics.csv*
    * *Top\_Unknown\_Barcodes.csv*
  * Analysis Status is now visible on the step.
* The integration service and integration-related properties have been moved from configuration files to database.
* Supports DRAGEN BCL Convert v4.2.7 analysis, including:
  * Cloud BCL Convert v4.2.7 running under the ICA Workflow Session Tracking application
  * Local BCL Convert v4.2.7

## Defect Repairs

* Demultiplexing stats are now correctly displayed in the Sample Details table in Demultiplexing step when the same samples with different indexes are in the run. For multi-lane flow cells, the demultiplexing stats are aggregated.
* The Validate Reagent Cartridge Barcode automation in the Load to Reagent Cartridge step now only accepts the \[A-Z]{2}\[0-9]{7}-\[A-Z0-9]{4} barcode format.

## Known Issues

* Sequencing run error triggered by disk space full on instrument causes *RunParameters.xml* to be empty and the run event cannot be processed on Clarity LIMS. This error is unlikely to occur as pre-run checks on the instrument check for sufficient disk space before run is started.
* [Sample sheet and planned run generation will fail](https://help.connected.illumina.com/clarity-lims/known-issues/integration/set9561-sample-sheet-generation-fail-samples-with-qc) if any of the samples in the pools has been assigned QC flag in prior steps before entering the Load to Reagent Cartridge step.

## Revision History

| **Version** | **Changes**                                                                              |
| ----------- | ---------------------------------------------------------------------------------------- |
| 2           | <ul><li>Updated Compatibility section to reference Compatibility matrix table.</li></ul> |
| 1           | <ul><li>Initial release.</li></ul>                                                       |


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