What's New

Date: August 2026

The latest releases introduce new updates to sequencing instrument integration support, expanded sequencing capabilities, and workflow usability improvements. It also resolves several defects that affected metrics reporting and workflow automation.

Clarity LIMS v6.3.5

Clarity LIMS v6.3.5 delivers product updates, fixes and security improvements

• Updated PostgreSQL to version 15.18 to maintain platform stability and security

• Upgraded the LabLink Angular framework to a modern version (v21.2) to improve performance and maintainability

• Improved LabLink page display and usability for custom dropdown fields with large option sets causing the option list to overflow the screen and obscure selectable options.

• Improved project handling in Lablink to prevent temporary projects from appearing in Advanced Search results when project creation is unsuccessful.

• Addressed general security vulnerabilities across the platform

• Improved support for downloading files and folders from remote HTTP and HTTPS storage locations in Clarity LIMS v6.3.2 and later.

The NovaSeq X Series workflows for Cloud-hosted and On-Premises deployments have been consolidated into a single unified workflow. This simplifies configuration management and ensures consistent behavior across deployment types.

Clarity LIMS now supports pool of pools workflows for NovaSeq X Series runs. Customers who perform pooling at the library preparation stage (prior to the bulk pooling step) can now manage and route those pre-pooled samples directly within Clarity LIMS without manual workarounds.

A new Skip Pooling option is available in the Assign ACT step to route samples that have already been pooled during library prep directly to the Dilute and Denature step.

Customers can now assign a Sample Project value to individual samples within Clarity LIMS. When Sample Project is specified, it is included in the generated sample sheet to enable BCL Convert to separate FASTQ output files into project-specific subdirectories.

Clarity LIMS now parses and displays per-lane sequencing run metrics for NovaSeq X Series instruments upon run completion. Previously, only per-run (aggregate) metrics were available.

Clarity LIMS supports creating a planned sequencing run with no analysis. The Clarity workflow will only track sequencing run status and primary metrics and analysis step is skipped.

The NovaSeq X Series 1.5B flowcell now supports the 600-cycle sequencing kit in Clarity LIMS. The cycle preset options have been expanded accordingly.

• System software v1.4 or newer is required for the 2 × 300 1.5B flow cell.

Clarity LIMS now supports the new 5B flowcell for NovaSeq X Series instruments. The 5B flowcell supports 100, 200, and 300-cycle kits and follows the same dilution and denature protocol as the 10B flowcell.

• System software v1.4 or newer is required for the 5B flow cell.

The sequencing run metrics displayed in Clarity LIMS for NextSeq 1000/2000 instruments have been updated to show Occupancy (%) in place of the Density metric. Occupancy is a more relevant and actionable metric for NextSeq 1000/2000 users when evaluating run quality.

Clarity LIMS software is a powerful laboratory information management system (LIMS) designed to optimize genomics sample and workflow management. It enables labs to track samples, streamline complex tasks, generate sample sheets, and identify poor-quality samples before they reach the sequencing system.

• Saves time and minimizes errors in sample handling through an automated workflow.

• Out-of-the box integration with Illumina instruments. Accelerate adoption of Illumina NGS and array protocols with preconfigured workflows that require no coding experience.

• Designed with compliance features including data entry validation, workflow enforcement, audit trails, electronic signatures and role-based permissions.

• Easily collect and share data in real-time with external clients via LabLink. Collaborate on sample submission, status, and results delivery in a single, secure environment.

Published: July 30, 2024

Vulnerability CVE-2024-6387 was found to allow an unauthenticated remote code execution in OpenSSH’s server (sshd) that grants full root access. It affects the default configuration and does not require user interaction, posing a significant exploit risk.

The vulnerability affects OpenSSH version:

• < 4.4p1 (unless the version is patched for CVE-2006-5051 and CVE-2008-4109)

• >= 8.5p1

Published: Aug 15, 2025

We want to provide an update to you about a recent service interruption that affected Clarity hosted instances. The issue was first reported on 17 July 2025 (0210 UTC) and fully resolved on 17 July 2025 (1315 UTC). You might have had encountered slowness within Clarity LIMS or Clarity LIMS failed to start during the period.

The issue was due to Illumina's managed HashiCorp Vault cluster service outage. The HashiCorp Vault outage was caused by surge in the number of active leases¹. All services have been restored with corrective and preventive actions in place. Additional monitoring and alerting have been added to ensure future stability.

We sincerely apologize for the disruption and impact that was caused to your operations.

Please contact Illumina tech support team should you have any question.

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