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DNAnexus vs Thermo SampleManager LIMS

DNAnexus logo

DNAnexus

Research

Regulated cloud platform for genomic and multiomic data, with GxP and FedRAMP coverage

From
On request
Rated
-
Full reviewWebsite
Thermo SampleManager LIMS logo

Thermo SampleManager LIMS

Research

Enterprise LIMS for regulated QC laboratories, with LES and SDMS in one product

From
On request
Rated
-
Full reviewWebsite

The short version

  • Each has a real cost: DNAnexus no pricing is published, so an organisation cannot compare the total cost against running the same pipelines on its own cloud account until it is deep in a sales process.; Thermo SampleManager LIMS no pricing is published in any form, and Thermo Fisher routes even basic cost questions through a request for quote, so early stage budget planning is guesswork.
  • They diverge on capability: DNAnexus covers Governed data storage, Thermo SampleManager LIMS covers Sample lifecycle management.
  • Prices and features above were last checked on 31 August 2026.

Where they differ

Only the attributes on which DNAnexus and Thermo SampleManager LIMS actually diverge.

Attributes where DNAnexus and Thermo SampleManager LIMS differ
AttributeDNAnexusThermo SampleManager LIMS
PlatformsWeb, LinuxWeb, Windows, Linux

Identical on both: starting price (On request), pricing model (quote), free tier (No), user rating (Not yet rated), category (Research).

What each one covers

Drawn from each product's published feature list. An absence here means we hold no record of it - not that the product lacks it.

Only in DNAnexus

  • Governed data storage
  • Workflow execution
  • App building
  • Controlled collaboration
  • Compliance posture
  • Cohort browsing

Only in Thermo SampleManager LIMS

  • Sample lifecycle management
  • Specifications and OOS handling
  • Laboratory execution system
  • Scientific data management
  • Stability studies
  • Instrument management
  • Environmental monitoring

What people use each for

The jobs each tool is most often brought in to do.

DNAnexus

  • A clinical diagnostics laboratory that needs a CLIA and CAP aligned environment for production sequencing pipelines without building the compliance evidence itselfnot Thermo SampleManager LIMS
  • A pharma sponsor analysing genomic endpoints in a registrational programme where 21 CFR Part 11 records are requirednot Thermo SampleManager LIMS
  • A biobank or consortium giving hundreds of external researchers governed access to a dataset too large to distributenot Thermo SampleManager LIMS
  • A diagnostics vendor packaging its pipeline as a versioned app so partner laboratories can run it without receiving the source codenot Thermo SampleManager LIMS

Thermo SampleManager LIMS

  • A pharmaceutical QC laboratory that needs enforced method execution and electronic signatures for GMP release testingnot DNAnexus
  • A multi site chemical or petrochemical business standardising sample handling and specifications across laboratoriesnot DNAnexus
  • A water or environmental testing laboratory with high sample throughput and regulatory reporting obligationsnot DNAnexus
  • A laboratory replacing a LIMS plus separate LES and SDMS estate and wanting to retire two integrations along with the old systemnot DNAnexus

Where each one falls short

Documented limitations, not opinions. Every one is a constraint you would hit in normal use.

DNAnexus

  • No pricing is published, so an organisation cannot compare the total cost against running the same pipelines on its own cloud account until it is deep in a sales process.
  • Compute and storage are billed through the platform rather than at underlying cloud list price, so the compliance envelope carries a persistent margin on every terabyte and core hour, which grows with the science rather than staying fixed.
  • Data egress at genomic scale is slow and chargeable, so leaving the platform later is a real project rather than a contract decision, and that gravity weakens negotiating position at renewal.
  • The regulated and validated configurations sit in a higher commercial tier than the research configuration, so an organisation that starts in research mode and later needs GxP faces a repricing rather than a setting change.
  • Bioinformaticians used to running Nextflow on their own infrastructure find the platform abstractions constraining, and porting an existing pipeline into the app model is engineering work that does not carry over to any other platform.

Thermo SampleManager LIMS

  • No pricing is published in any form, and Thermo Fisher routes even basic cost questions through a request for quote, so early stage budget planning is guesswork.
  • Implementation is configuration heavy and normally requires Thermo Fisher professional services or a specialist partner, and services costs routinely exceed the licence cost in the first year.
  • Computer system validation is the customer responsibility on top of implementation, so a GMP laboratory carries a validation programme of its own before go live and repeats a subset of it at every upgrade.
  • Cloud hosting is charged as an annual fee scaled to licence count, so seats drive infrastructure cost as well as licence cost and occasional users are expensive twice.
  • The product carries a long codebase history and its configuration model is specialist, which makes in house administrators hard to recruit and creates a dependency on external consultants for changes that would be self service in a newer LIMS.

Pricing, plan by plan

DNAnexus

On request
  • DNAnexus Platform$undefined/year
    • Quoted per organisation through a sales process
    • Storage and compute billed through the platform rather than at cloud list price
    • Regulated and validated configurations are a separate commercial tier

Thermo SampleManager LIMS

On request
  • SampleManager LIMS$undefined/year
    • Quoted through the Thermo Fisher sales team, nothing published
    • Annual hosting fee calculated on the number of licences for cloud deployments
    • Deployment as Thermo managed AWS, on premise, or customer cloud

Which should you pick?

Choose DNAnexus if

  • You need governed data storage.
  • You work on Web, Linux.
  • You also want workflow execution.
DNAnexus review

Choose Thermo SampleManager LIMS if

  • You need sample lifecycle management.
  • You work on Web, Windows, Linux.
  • You also want specifications and oos handling.
Thermo SampleManager LIMS review

Questions people ask

Is DNAnexus or Thermo SampleManager LIMS better?
Neither clearly leads. DNAnexus starts at On request and Thermo SampleManager LIMS at On request, and user ratings are close enough to be indistinguishable. Choose on capability and platform support.
Which is cheaper, DNAnexus or Thermo SampleManager LIMS?
DNAnexus starts at On request and Thermo SampleManager LIMS at On request.
Does DNAnexus or Thermo SampleManager LIMS run on more platforms?
DNAnexus runs on Web, Linux. Thermo SampleManager LIMS runs on Web, Windows, Linux.
What is DNAnexus best used for?
DNAnexus is most often used for a clinical diagnostics laboratory that needs a clia and cap aligned environment for production sequencing pipelines without building the compliance evidence itself, a pharma sponsor analysing genomic endpoints in a registrational programme where 21 cfr part 11 records are required, a biobank or consortium giving hundreds of external researchers governed access to a dataset too large to distribute, a diagnostics vendor packaging its pipeline as a versioned app so partner laboratories can run it without receiving the source code. Of those, a clinical diagnostics laboratory that needs a clia and cap aligned environment for production sequencing pipelines without building the compliance evidence itself and a pharma sponsor analysing genomic endpoints in a registrational programme where 21 cfr part 11 records are required are not what Thermo SampleManager LIMS is typically brought in for.
What can DNAnexus do that Thermo SampleManager LIMS cannot?
DNAnexus covers Governed data storage, Workflow execution, App building, Controlled collaboration. Thermo SampleManager LIMS covers Sample lifecycle management, Specifications and OOS handling, Laboratory execution system, Scientific data management.

Answered from the vendors’ own pages

DNAnexus: Why pay for DNAnexus instead of raw AWS?

For the compliance evidence. GxP, FedRAMP, CLIA, CAP and Part 11 coverage removes a validation programme most organisations would otherwise have to build and maintain themselves.

Thermo SampleManager LIMS: Does SampleManager include LES and SDMS?

Yes. Laboratory execution and scientific data management are part of the product rather than separate purchases, which removes two integration projects.

DNAnexus: Is validated use included?

No. Regulated and validated configurations sit in a separate commercial tier from ordinary research use.

Thermo SampleManager LIMS: How much does it cost?

Nothing is published. Pricing is quoted, and cloud deployments carry an annual hosting fee based on licence count.

DNAnexus: Can I get my data out?

Yes, but egress at genomic scale is chargeable and slow, so plan exit costs at the point of signing.

Thermo SampleManager LIMS: Is it validated when I buy it?

Thermo Fisher supplies qualification documentation, but computer system validation of your configured instance remains your responsibility.

DNAnexus: Does it host UK Biobank?

Yes, DNAnexus hosts the UK Biobank research analysis platform, which has its own access approval and cost terms.

Thermo SampleManager LIMS: Can I run it on premise?

Yes. Thermo managed AWS, on premise and customer cloud deployments are all offered.

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