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Release Notes

Published: Apr 15, 2020

Latest Patch: v5.3.0

This release is only for Clarity LIMS in the cloud-based environment and it is focused on the following:

LabLink, a sample submission portal

This feature allow external collaborators to use LabLink to submit samples to the lab that is using Clarity LIMS, and view status and results within LabLink.

Illumina Preset Protocols v1.0.0

This package includes pre-set Illumina library prep protocols, integration workflows for Illumina instruments and a standard set of QC protocols and steps. All the pre-set protocols and workflows provide a good starting for users to create workflows specific to individual lab processes.

Security improvements to the application preventing various attacks and other safety that may potentially expose the inner state of the product.


Documentation for BaseSpace Clarity LIMS v5.3 can be found here:

BaseSpace Clarity LIMS v5.3 Online Help

If you have any questions or require assistance, please email techsupport@illumina.com

General Notes

The Clarity LIMS v5.3 will only be supporting Cloud-based environment.

The LabLink feature does not support LDAP integration.

The Clarity LIMS Operations Interface has been deprecated and is no longer available in BaseSpace Clarity LIMS 5.0 onwards.

For API related information, see the API Portal, and refer to the changes in Current Revision section. If you have created scripts using our pre-release API endpoints, please contact us for a complete change list to ensure your scripts continue to function.



LabLink is a sample submission portal that is part of Clarity LIMS. LabLink allows external collaborator to submit samples and the information will be reflected in Clarity LIMS for the lab that is using Clarity LIMS. The features developed in LabLink are as following:

Ability to submit project/sample in an orderly way.

Ability to view status of a project/sample and download results.

Ability to add a note or upload a document to a project/sample.

Ability to search for a project name or sample name from the search box.

Ability to download Resource Materials. These are the documents uploaded by Lab Administrator and can be stored in Resource Materials section. It can be sample submission templates, shipping instructions etc.

Ability to request for a user ID from login page.

Increased password security requirement.

Introduced CAPTCHA check.

Improved user experience design.

On top of the above, additional features for Administrators role in LabLink are as following:

Ability to share documents and stored as Resource Materials.

Ability to mark Custom Fields to be visible in LabLink.

Ability to modify Disclaimers displayed when user creates a project or request for a user ID.

Ability to modify Contact Us information.

Ability to assign a unique user ID to the new user before approving the user request. Requester will not be able to create user ID themselves. The LabLink User Approval Workflow will now be in LabLink instead of Operations Interface.

Ability to access to projects and samples created by all collaborators.

Illumina Preset Protocols v1.0.0

This package is compatible with:

BaseSpace Clarity LIMS v5.1 or later

NGS Extensions Package v5.19 or later

The pre-set protocols included in this release:

Preset protocols for Illumina library prep kits.





Preset Integration workflows for Illumina Instruments.


NextSeq 500/550

NextSeq 1000/2000

NovaSeq 6000

Library Prep Validation

QC Protocols

Clarity LIMS Configuration

Added a new token expression to {InputWellLocation} to allow user to specify the start and end index. Refer to Derived Sample Naming Convention Tokens.

Security Improvements

Increased security measures to prevent account enumeration attacks, information leakage and to prevent attackers from disclosing sensitive data and gaining elevated access-privileges to sensitive page content.

Bugs Fixed


Affects Version/s

Updating endpoint script will change the API URI format.

4.2.23, 5.1.5

Toggle switch was set yes as default, the toggle field is not checked.

5.2.0, 5.1.5

Hidden Step UDF will revert to default value on Save or NextStep.


Known Issues

Cannot move to Next Step when uploading a measurement file to Standard QC step artifact.

Unable to handle large pools of samples (approx. 4000) from Clarity LIMS UI in pool creation or the creation of output container.

In AUTOMATED – NovaSeq Run step of NovaSeq 6000 v3.0 workflow, the lane number of individual samples in the library pool is assigned according to the LIMSID order instead of the well position.