BaseSpace Clarity LIMS (Laboratory Information Management System)

BaseSpace Clarity LIMS is a laboratory information management system that helps laboratories track samples and optimize procedures and workflows.

As a key component of the BaseSpace Suite, BaseSpace Clarity LIMS does much more than track laboratory samples. BaseSpace Clarity LIMS supports regulatory compliance yet remains flexible to accommodate new technologies and workflows. It scales and integrates with your laboratory’s ecosystem and automates routine tasks. BaseSpace Clarity LIMS:

  • Supports compliance with eSignature, audit trails, reagent and lot tracking, and privacy and security controls
  • Helps your laboratory reduce time with straightforward implementation, reporting, preconfigured workflows for common instruments, and quality control features that flag poor-quality samples
  • Promotes accuracy with automation and built-in business logic and error checking
  • Manages complexity and change with integrations and workflows for qPCR, microarrays, and sequencing and the ability to create new workflows when needed
  • Scales to accommodate increased sample volumes with different editions and on-site or cloud-based implementations
  • Eases IT burden with no additional upgrade fees, quick implementation, and rigorous security practices (for cloud-based implementations)
  • Enables thorough customization to your laboratory environment through use of the application programming interface (API)
Sample tracking and audit readiness

BaseSpace Clarity LIMS provides receipt-to-result sample tracking, comprehensive lab operation reporting, and human-readable audit trails.

Preconfigured workflows and out-of- the-box integrations

BaseSpace Clarity LIMS includes preconfigured workflows to support many common genomics applications. Additionally, out-of-the-box integrations with common laboratory and sequencing instruments are available for quick implementation.

Flexibility and scalability

BaseSpace Clarity LIMS enables you to easily build new workflows that reflect laboratory protocols. Further, different editions and a comprehensive application programming interface (API) enable the LIMS to scale to increased sample volumes or new instruments.


Silver Edition

Gold Edition

X Edition

Sample tracking
Sample sheet generation
Single user access
Visual pooling and adapter assignment
Community forum
Reagents and controls tracking
QC tracking
Collaboration portal
Overview Dashboards
Over 40 preconfigured workflows
Ready to use lab operation reports
Instrument tracking  
Application Programming Interface (API)  
Out of the box Instrument integrations  
Integration with HiSeq X Series, Microlab STAR, Spectromax, LabGx, LightCycler 480, and cBot    
2 automated HiSeq X Series workflows with business logic to minimize hands-on time    
Automated sample QC    
Reagent verification    
Pipelining to HiSeq Analysis Software (HAS)    
Full support from Illumina and Hamilton    
Phone support
Hosted or on-premise version available

Customer Stories

See the Product


Integrate BaseSpace Clarity LIMS with your Illumina systems, qPCR, microarray, fluorometer/spectrophotometer, and other laboratory instruments.

Browse All Integrations

BaseSpace Clarity LIMS Integrations

What is a LIMS?

Infographic | PDF (<1 MB)
A laboratory information management system (LIMS) is software that enables secure, automated, scalable tracking and information management. This infographic shows the benefits of a LIMS.

Selecting a LIMS

Infographic | PNG (<1 MB)
Purchasing a LIMS is a significant investment with long-term implications. View our infographic to learn about the questions you should be asking when selecting a LIMS.

Support and Developer Resources


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BaseSpace Clarity LIMS version 5.0 is now available.