Illumina Clarity LIMS overview
Short profile: documented facts and what independent sources report, without editorial assessment. How we build profiles
Clarity LIMS is Illumina's LIMS for genomics labs. It tracks samples from receipt to result, connects to Illumina instruments, takes submissions through its LabLink portal and supports step-level e-signatures. It runs on premises or in a cloud managed by Illumina, on annual subscriptions without published prices. Documented users include sequencing cores, the CDC and a UK health trust.
Clarity LIMS key facts
| Origin and names | Built by GenoLogics, which relaunched its Geneus LIMS as Clarity LIMS in 2012. Illumina announced its acquisition of GenoLogics on 4 August 2015 and completed it in early September 2015. Former names: GenoLogics Clarity LIMS, BaseSpace Clarity LIMS; Clarity LIMS X was a 2015 edition. Unrelated to DataApex Clarity. |
|---|---|
| Price | Not published. Two subscription plans, renewed annually: Professional (one instance, three named users) and Enterprise (two instances, ten named users), quoted by Illumina sales representatives. Public documents give price references. |
| Hosting | On premises, or in a cloud Illumina deploys, maintains and scales; Illumina lists Clarity LIMS among its informatics tools using AWS. No hosting region is stated. Data is held in PostgreSQL. |
| Implementation | Not published. The data sheet lists a one-time onboarding item for each plan, with no stated duration. |
| Compliance | For CLIA-certified and other regulated labs, Illumina lists audit trail, e-signatures, role-based permissions and data entry and workflow enforcement; the documentation details step-level signing. HIPAA business associate agreement with Enterprise, US only. ISO/IEC 27001 and 27701 listed for the cloud instance. |
| Sample submission | LabLink, part of Clarity LIMS, lets principal investigators, clinicians and external labs submit samples, and lets the lab send them progress updates and publish files. |
| Who uses it | Sequencing facilities at Michigan State University, Virginia Tech and SickKids' Centre for Applied Genomics publish instructions for their Clarity LIMS portals. APHL's 2022 influenza sequencing call describes the CDC's use. Belfast Health and Social Care Trust contracted it in 2021 for its pathogen sequencing service. |
Clarity LIMS pricing and editions
No public price list: quote only. Illumina publishes two subscription plans renewed annually, Professional and Enterprise, with their instance and named-user counts and features, but no price on the product page, the data sheet or the flyer. Additional named users, test instances and one-time onboarding are separate order items, also without prices.
| Plan | For | Price | What it includes |
|---|---|---|---|
| Professional | On quote | Sample traceability, prepackaged Illumina workflows, instrument integrations, dashboards, API access and LabLink sample submission, local or cloud deployment; one instance and three named users. [17] | |
| Enterprise | On quote | Everything in Professional plus LDAP single sign-on and a HIPAA business associate agreement (US only); two instances and ten named users. [17] |
Prices in public records
Clarity LIMS publishes no price list. Public documents give price benchmarks; amounts are not reproduced here, and the documents can be read at their source:
- Procurement of Illumina Clarity LIMS system to support Regional Pathogen Sequencing Service (contract award notice 022772-2021), Belfast Health and Social Care Trust (Find a Tender) [11]
Conditions and limits
- Subscriptions are renewed annually. [17]
- The HIPAA business associate agreement is offered for the US only. [17]
- Onboarding is sold as a separate one-time item for each plan. [17]
Clarity LIMS compliance and security
Vendor-documented: a dedicated vendor page or documentation article describes it. Vendor-stated: the vendor states it without describing it in detail. Not mentioned: found neither in the vendor's material nor in independent sources.
| Standard | Evidence | What we found |
|---|---|---|
| CLIA | Vendor-stated | The product page lists, for CLIA-certified organizations and other regulated labs, data entry enforcement, workflow enforcement, issue resolution documentation, precision monitoring, role-based permissions, audit trail and electronic signatures, without describing them. The documentation describes step-level electronic signatures on a separate page, without reference to CLIA. [16] |
| HIPAA | Vendor-stated | A HIPAA business associate agreement (BAA) is listed with the Enterprise plan only, for the US only. [17] |
| 21 CFR Part 11 | Not mentioned | |
| EU GMP Annex 11 | Not mentioned | |
| ISO/IEC 17025 | Not mentioned | |
| GAMP 5 | Not mentioned | |
| GDPR | Not mentioned | |
| ISO 15189 | Not mentioned |
Security and hosting details (4)
- Hosting: Illumina presents Clarity LIMS among its informatics tools using AWS; no hosting region is stated for Clarity. [26]
- ISO/IEC 27001:2013 certification listed for the cloud instance, in both plans (cloud instance only). [17]
- ISO/IEC 27701:2019 certification listed for the cloud instance, in both plans (cloud instance only). [17]
- The 2025 flyer describes a certified environment under ISO/IEC 27001:2022 and ISO/IEC 27701:2019, without naming the deployment it covers. [18]
What Clarity LIMS is
Clarity LIMS is the laboratory information management system Illumina sells to genomics laboratories to track samples and manage workflows. Each sample entered receives a unique LIMS ID and moves through preconfigured workflows for Illumina sequencing and array applications: more than 60 on the product page, over 65 in the 2025 flyer. Integration packages connect the LIMS to Illumina instruments. For the NovaSeq 6000, the package validates the run setup, generates the sample sheet, starts the step automatically and parses run data back into Clarity LIMS. Dashboards show how many samples are in progress across the lab, and the data sheet lists reagent lot and barcode tracking among the compliance features.
The product comes from GenoLogics Life Sciences Software, a company with an office in Victoria, British Columbia. GenoLogics sold Geneus LIMS, then revamped and relaunched it as Clarity LIMS in 2012; GenomeWeb described the new version at its launch as designed to manage sequencing data in CLIA-regulated environments and research settings. Illumina led an investment round in GenoLogics in 2011 and signed a co-selling agreement with it before announcing, on 4 August 2015, an agreement to acquire the company. At that announcement, Illumina said Clarity LIMS had been adopted by over 120 genomic labs worldwide. The acquisition was completed in early September 2015. GenomeWeb reported that GenoLogics would keep its Victoria office and its 60 employees, join Illumina’s enterprise informatics business unit and continue to offer Clarity LIMS as a standalone product.
Clarity LIMS has no connection with Clarity, the chromatography data system sold by DataApex.
How it is sold and run
Both subscription plans include sample traceability, Illumina workflows and instrument integrations, dashboards, API access with toolkits, LabLink, workflow configuration in the web interface and read-only database access. Enterprise has two instances instead of one and ten named users instead of three, and adds LDAP single sign-on and a HIPAA business associate agreement for the US. The administration guide has pages on LDAP integration and on integration with the Illumina Connected Software platform.
In the cloud, Illumina deploys and maintains the system and scales the hardware as required. Illumina’s technical overview describes the stack: a Java core with PostgreSQL, Apache Tomcat 9.0, Apache, ElasticSearch and RabbitMQ, plus the Automation Worker. For support, the data sheet cites documentation, how-to videos and example cookbooks for the API and configuration; no support levels or response times are published.
What has changed
GenoLogics released Clarity LIMS 3.1 in August 2014 and, in July 2015, Clarity LIMS X, an edition built for Illumina SeqLab and HiSeq X systems; Fierce Biotech reported that GenoLogics supplied the LIMS for HiSeq X Ten systems. The current product page offers only the Professional and Enterprise plans. Under the BaseSpace Clarity LIMS name, Illumina announced in March 2022 the end of the Reporting Module, with no renewals and no further updates or support, and ended support for versions 4.0 to 5.1 on 15 June 2022, keeping version 6.0 as the line in development. The 2025 flyer refers reporting and analytics to Emedgene and Connected Analytics. Version 6.3.5, published in June 2026, is a maintenance release that qualifies PostgreSQL 15.18, updates a LabLink library and fixes security issues, with no new features.
Who documents using it
Three sequencing facilities, at two universities and a children’s hospital, publish instructions for their Clarity LIMS portals. Michigan State University’s Genomics Core uses it for sequencing orders, sample information and progress tracking; the Fralin Life Sciences Institute at Virginia Tech takes Sanger sequencing submissions through LabLink; and The Centre for Applied Genomics at SickKids in Toronto uses it for ordering services, tracking sample status and retrieving data.
Public health use appears in two procurement records. In its November 2022 call for influenza sequencing centres, issued with the CDC’s influenza division, the Association of Public Health Laboratories wrote that the CDC has used Clarity LIMS to understand how viruses were processed and handled in its NGS pipeline, managing the workflow rather than holding comprehensive patient sample metadata, and that selected sites would use a cloud-hosted version from APHL connected to the AIMS cloud. In Northern Ireland, Belfast Health and Social Care Trust awarded Illumina UK a contract on 8 September 2021 for the Clarity LIMS system behind its SARS-CoV-2 sequencing service, without a call for competition, on the grounds that the system is available only from Illumina and integrated with the Illumina reagent kits and instrument systems of its ALMS contract.
Clinical use shows in two 2017 job postings from Leidos for the National Cancer Institute’s ClinOmics programme, which described configuring and maintaining Clarity LIMS to track clinical samples through wet-bench and computational protocols; one required experience developing and maintaining it in a clinical laboratory, and both stated they did not represent a current opening. A 2016 review in the European Journal of Human Genetics names Clarity LIMS among commercial systems tailored to NGS workflows in clinical laboratories. GenoLogics itself announced in April 2015 that GenomeDx Biosciences had implemented the cloud version in its CLIA-certified San Diego laboratory, and in other announcements that SciLifeLab was implementing it in its clinical genomics lab in Sweden, and that Genomic Health had selected it for next-generation sequencing workflows.
Clarity LIMS capabilities
| Capability | Evidence | What the source describes |
|---|---|---|
| Client portal | Vendor-documented | LabLink lets the lab's end users (principal investigators, clinicians, external labs) submit samples, and lets the lab send progress updates and publish files to them. [21] |
| Instrument integration | Vendor-documented | Integration packages for Illumina instruments: for NovaSeq 6000, run setup validation, sample sheet generation, automatic step start and parsing of run data back into the LIMS. [22] |
| Sample management | Vendor-documented | Each sample gets a unique LIMS ID and is tracked from receipt to result with real-time status, through preconfigured Illumina sequencing and array workflows. [17] |
| Inventory | Vendor-stated | Reagent lot and barcode tracking is listed among the compliance features. [17] |
| Reporting | Vendor-stated | Dashboards show how many samples are in progress across the lab; the former Reporting Module was withdrawn in 2022. [17] |
All 5 other features
| Feature | Evidence | What the source describes |
|---|---|---|
| Electronic signature sign-off per step | Vendor-documented | Steps can require an eSignature (username and password) before completion; signing is a role-based permission, users cannot sign their own work by default, and every attempt is logged. [20] |
| API and Automation Worker scripting | Vendor-documented | An Application Programming Interface and the Automation Worker (Windows service or Linux daemon) run scripts that automate and extend the LIMS. [19] |
| Preconfigured Illumina workflows | Vendor-stated | Ships with more than 60 preconfigured workflows for Illumina NGS and array applications (over 65 in the 2025 flyer). [16] |
| Workflow and data entry enforcement | Vendor-stated | Data entry validation and workflow enforcement are listed as compliance features, alongside role-based permissions. [18] |
| LDAP single sign-on | Vendor-stated | LDAP single sign-on, part of the Enterprise plan; the administration guide has a dedicated LDAP integration page. [16] |
What independent sources say about Clarity LIMS
Documented deployments
- Michigan State University, Research Technology Support Facility Genomics Core: uses Clarity LIMS so that its users can create sequencing orders, submit sample information and track progress. [6]
- Virginia Tech, Fralin Life Sciences Institute Genomics Sequencing Center: takes sample submissions through a Clarity LIMS LabLink portal. [7]
- The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Toronto: uses Clarity LIMS for online ordering of services, sample status tracking and data retrieval. [8]
- U.S. Centers for Disease Control and Prevention (influenza next-generation sequencing): has used Clarity LIMS to understand how viruses were processed and handled in its NGS pipeline, according to the APHL influenza sequencing centre RFP answers. [9]
- Belfast Health and Social Care Trust (Northern Ireland): awarded Illumina UK a contract, without a call for competition, for the Clarity LIMS system supporting its Regional Pathogen Sequencing Service (SARS-CoV-2). [11]
- Leidos, for the National Cancer Institute's ClinOmics programme: recruited in 2017 for roles that configure and maintain Clarity LIMS to track clinical samples through wet-lab and computational protocols, one of them requiring Clarity LIMS experience. [13]
- Leidos, for the National Cancer Institute's ClinOmics programme (February 2017 posting): advertised a bioinformatics analyst role to configure and maintain Clarity LIMS, with prior Clarity LIMS experience preferred. [12]
Other findings from independent sources (6)
- GenomeWeb reported at the 2012 launch that GenoLogics customers who tested the beta version of Clarity, at a Max Planck institute and at QCMC, praised its user-friendly interface, while noting they had tested only a limited version. [4]
- GenomeWeb reported in 2015 that GenoLogics' customers included early-stage molecular diagnostics companies and hospital laboratories, naming SciLifeLab, GenomeDx and Personalis. [3]
- Fierce Biotech reported that GenoLogics supplied the LIMS for Illumina's HiSeq X Ten systems when Illumina agreed to buy it in 2015. [1]
- A 2016 review in the European Journal of Human Genetics names Clarity LIMS among the commercial systems tailored to NGS workflows in clinical laboratories. [5]
- Belfast Health and Social Care Trust justified a direct award on the grounds that Clarity LIMS is available only from Illumina and is integrated with Illumina reagent kits and instruments. [10]
- In the APHL influenza sequencing centre RFP, CDC described its Clarity LIMS use as managing the NGS workflow process rather than holding comprehensive patient sample metadata. [9]
User reviews
- TrustRadius (Clarity LIMS Gold): no reviews, as of 2026-10-19. [14]
- SelectScience: no reviews, as of 2026-10-19. [15]
Alternatives to Clarity LIMS
| Alternative | Deployment | Pricing | Why consider it |
|---|---|---|---|
 Sapio LIMS | Cloud, On-premise | Quote only | A 2016 review in the European Journal of Human Genetics names Sapio's Exemplar LIMS alongside Clarity LIMS among the commercial systems tailored to NGS workflows in clinical laboratories. |
 Agilent SLIMS | Cloud, On-premise | Quote only | Also used for sequencing by UK health bodies: UKHSA's 2025 contract notice calls SLIMS a critical dependency of its sequencing labs, while Belfast's 2021 award ties Clarity LIMS to its pathogen sequencing service. |
 Clinisys Laboratory Solution | Cloud | Quote only | Offers Public Health and, in North America, Genomics packages on one laboratory platform, and Alaska and Michigan have chosen it for their state public health laboratories; Clarity LIMS's documented public health use is at the CDC. |
Clarity LIMS product and company details
| Vendor | Illumina, Inc., San Diego, California, USA |
|---|---|
| Deployment | Cloud, On-premise |
| Hosting | Cloud deployed, maintained and scaled by Illumina, which lists Clarity LIMS among its informatics tools using AWS (no region stated), or on-premises installation; PostgreSQL database |
| Latest version | Version 6.3.5, 2026-06-01 |
| Modules | Sample management, Instrument integration, Client portal, Reporting |
| Website | illumina.com |
Integrations (3)
Support and services (1)
- Documentation, how-to videos and example cookbooks for the API and configuration. [17]
Release history (3)
Company timeline and vendor figures (7)
Figures stated by the vendor:
- Adopted by over 120 genomic labs worldwide (Illumina figure at the 2015 acquisition announcement). [28]
- : Illumina withdrew the BaseSpace Clarity LIMS Reporting Module (no renewals, then no updates or support) and ended support for versions 4.0 to 5.1, leaving version 6.0 as the supported line. [25]
- : Illumina's third-quarter 2015 results release lists the completed acquisition of GenoLogics among its updates. [29]
- : Illumina completed the acquisition of GenoLogics in early September 2015. [3]
- : GenoLogics was to continue offering Clarity LIMS as a standalone product after joining Illumina. [3]
- : Illumina announced a definitive agreement to acquire GenoLogics Life Sciences Software, a developer of laboratory information management systems. [28]
- : Trade press reported the purchase price as undisclosed. [2]
Related pages
- Illumina Clarity LIMS alternatives
- Best LIMS for Genomics and Sequencing Labs
- How Much Does a LIMS Cost?
- LIMS Requirements Checklist
- LIMS Implementation Timeline: What the Phases Really Cost
Clarity LIMS FAQ
How much does Clarity LIMS cost for a lab with more than ten users?
Illumina publishes no price for either plan and refers buyers to a local Illumina sales representative. The Enterprise plan includes two instances and ten named users; the data sheet lists additional named-user packs and test instances as separate order items, all quoted rather than priced publicly.
Does Clarity LIMS support 21 CFR Part 11?
Illumina's product page, data sheet, flyer and electronic signature documentation do not name 21 CFR Part 11. The documentation describes step-level signing: a step can require the signer's username and password before completion, signing is a role-based permission, users cannot sign off their own work by default, changes made before the step is completed require a new signature, and every attempt, successful or not, is recorded with the step and in the audit trail. The page does not say whether a signature records its meaning. A BaseSpace Clarity LIMS Gold Validation Package, listed per year, appears in the catalogue of a reseller to US government buyers, which refers to another document for its contents. Worth asking Illumina how these controls map to Part 11 for your use.
Can Clarity LIMS connect to non-Illumina instruments?
The compatible instruments on the product page are all Illumina's: MiSeq, iSeq 100, MiniSeq, NextSeq 550, 1000 and 2000, NovaSeq 6000, NovaSeq X and X Plus, MiSeq i100 and i100 Plus and iScan, plus MiSeqDx, NextSeq 550Dx and NovaSeq 6000Dx in research mode. For third-party tools and instruments, Illumina points to the API; the Automation Worker, a Windows service or Linux daemon, runs scripts that automate and extend the LIMS.
Does the ISO 27001 certification cover an on-premises installation?
The plan table on the product page and in the 2023 data sheet lists ISO/IEC 27001:2013 and ISO/IEC 27701:2019 certification for the cloud instance, in both plans. The 2025 flyer describes a certified environment under ISO/IEC 27001:2022 and 27701:2019 without naming the deployment it covers. None of these documents lists a certification for on-premises installations.
Sources
15 independent sources and 20 vendor or vendor-supplied sources. A profile is published only when at least three independent publishers back it; this one has 9. See the methodology. Numbers match the references in the page.
Show all 35 sources
Independent sources
- Illumina strikes deal to buy LIMS provider GenoLogics, Fierce Biotech (accessed 2026-10-19)
- Illumina to Buy GenoLogics, GenomeWeb (accessed 2026-10-19)
- Joining Illumina Gives GenoLogics Broader Market Reach, Deeper Integration Options, GenomeWeb (accessed 2026-10-19)
- Setting its Sights on the Clinical Market, GenoLogics Updates LIMS for Regulated Environments, GenomeWeb (accessed 2026-10-19)
- New challenges for BRCA testing: a view from the diagnostic laboratory (European Journal of Human Genetics, 2016), European Journal of Human Genetics (Springer Nature) (accessed 2026-10-19)
- Order Submission, Research Technology Support Facility (Michigan State University), Michigan State University, Research Technology Support Facility (accessed 2026-10-19)
- Clarity LIMS Sample Submission Instructions (Genomics Sequencing Center, Fralin Life Sciences Institute), Virginia Tech, Fralin Life Sciences Institute (accessed 2026-10-19)
- TCAG Online ordering using LIMS, The Hospital for Sick Children (SickKids), The Centre for Applied Genomics (accessed 2026-10-19)
- Influenza Sequencing Center, request for proposals (questions and answers), Association of Public Health Laboratories (APHL) (accessed 2026-10-19)
- Procurement of Illumina Clarity LIMS system to support Regional Pathogen Sequencing Service (voluntary ex ante transparency notice 019040-2021), Belfast Health and Social Care Trust (Find a Tender) (accessed 2026-10-19)
- Procurement of Illumina Clarity LIMS system to support Regional Pathogen Sequencing Service (contract award notice 022772-2021), Belfast Health and Social Care Trust (Find a Tender) (accessed 2026-10-19)
- Bioinformatics Analyst – LIMS (NCI), Leidos (job posting), Leidos (job posting hosted by Texas A&M AgriLife TxGen) (accessed 2026-10-19)
- LIMS Developer (NCI), Leidos (job posting), Leidos (job posting hosted by Texas A&M AgriLife TxGen) (accessed 2026-10-19)
- Clarity LIMS Gold reviews on TrustRadius, TrustRadius (accessed 2026-10-19)
- GenoLogics company page (Clarity LIMS) on SelectScience, SelectScience (accessed 2026-10-19)
Vendor and vendor-supplied sources
- Clarity LIMS software | Improve lab productivity and efficiency, Illumina (accessed 2026-10-19)
- Clarity LIMS software data sheet (M-GL-01069 v3.0), Illumina (accessed 2026-10-19)
- Clarity LIMS flyer (M-GL-01921 v2.0), Illumina (accessed 2026-10-19)
- Clarity LIMS v6.2 and LabLink v2.4, Technical Overview, Illumina (accessed 2026-10-19)
- Clarity LIMS v6.3 and LabLink v2.5, Configure electronic signatures, Illumina (accessed 2026-10-19)
- LabLink v2.4 Reference Guide, Illumina (accessed 2026-10-19)
- NovaSeq 6000 Integration Package v3.6.0, User Interaction, Validation and Troubleshooting, Illumina (accessed 2026-10-19)
- Clarity LIMS v6.3 and LabLink v2.5, Administration, Illumina (accessed 2026-10-19)
- Release Notes Clarity LIMS v6.3.5, Illumina (accessed 2026-10-19)
- Product obsolescence notice PON2022-1226: end of life for the BaseSpace Clarity LIMS Reporting Module and select versions (M-AMR-00486), Illumina (accessed 2026-10-19)
- Amazon Web Services (AWS) partnership, Illumina (accessed 2026-10-19)
- About Illumina, Illumina (accessed 2026-10-19)
- Illumina Signs Agreement to Acquire GenoLogics, Leader in Genomics Laboratory Information Management System Market, Illumina (accessed 2026-10-19)
- Illumina reports financial results for third quarter of fiscal year 2015, Illumina (accessed 2026-10-19)
- GenoLogics Life Sciences Software Inc. Releases Clarity LIMS X As Part Of Illumina Seqlab, BioSpace, vendor-supplied content (accessed 2026-10-19)
- GenomeDx implements Clarity LIMS, 4/15 (CAP Today Marketplace), CAP Today (College of American Pathologists), vendor-supplied content (accessed 2026-10-19)
- GenomeDx Selects GenoLogics Clarity LIMS to Support Transcriptome Analysis, GenomeWeb, vendor-supplied content (accessed 2026-10-19)
- Swedish Institution Taps GenoLogics LIMS for NGS Analysis Support, GenomeWeb, vendor-supplied content (accessed 2026-10-19)
- Genomic Health Taps GenoLogics Clarity LIMS to Support Next-Gen Sequencing Workflows, GenomeWeb, vendor-supplied content (accessed 2026-10-19)
- BaseSpace Clarity LIMS Gold Validation Package (per year), part number 20006511, Government Scientific Source, vendor-supplied content (accessed 2026-10-19)