SeqOne Platform
SeqOne Platform is a CE-IVD certified genomic analysis suite for molecular laboratories. Its DiagAI scoring engine prioritises variants across germline, somatic and infectious disease panels, exomes and genomes, while SeqOne Flow automates the pipeline from sequencer to clinical report.
What is SeqOne Platform?
SeqOne Platform is a software-as-a-service application that molecular laboratories use to analyse and interpret next-generation sequencing data. It is published by SeqOne S.A.S., based in Montpellier, France, and reached through regional instances for Europe, the United States, Australia, Switzerland, the United Kingdom and Canada. The terms of use describe it as accessible remotely in the cloud and, optionally, locally.
The platform is wet-lab and sequencer agnostic. It handles targeted panels, whole exomes and whole genomes, from short-read and long-read chemistries alike, and it covers three application families: oncology (solid tumours, liquid biopsy, haematology, hereditary cancers), inherited diseases (rare diseases, inherited disorders, carrier screening) and infectious diseases (viral and bacterial pathogens, antimicrobial resistance, gene function prediction).
Its interpretation engine is DiagAI, a 0-to-100 score combining pathogenicity prediction, phenotype matching against HPO terms and expert-authored rules. The publisher reports that DiagAI surfaces 96% of diagnostic variants within an average shortlist of eight candidates, that its SmartPick suggestion reaches 92% specificity, and that 90% of causal variants rank in the top three. A peer-reviewed evaluation reports 94.9% on exomes, and a run on 565 Genomics England whole-genome cases placed 98% of causal variants within ten candidates. A dedicated classifier, UP2-SV, extends the same ranking to structural variants and CNVs.
Around that engine sit automated quality checks on coverage, contamination, kinship and sample identity, workset versioning, ACMG, REVEL, CI-SpliceAI and AlphaMissense classifications, AMP Tier oncogenicity, annotation from more than fifty public sources plus optional CKB Boost and COSMIC, and genomic signatures including MSI, TMB, clonality and HRD status. GenomeAlert! re-evaluates stored variant classifications monthly against ClinVar. SeqOne Flow automates the pipeline itself, triggering project creation, sample import and analysis launch from API, file or e-mail events, and connecting to laboratory information management systems.
The platform is an in vitro diagnostic medical device, CE-IVD Class C certified under the EU IVDR, and its publisher holds ISO 13485, ISO 27001 and HDS certification. The homepage claims more than 1,000 biologists and geneticists, over 160 clinical and research laboratories across more than 30 countries, and roughly 200,000 genomic tests supported each year.
What it does
- Rank the variants of a case with the DiagAI score and its explainable 0-to-100 output
- Run secondary and tertiary analysis on panels, whole exomes and whole genomes
- Check data integrity before interpretation, with coverage, contamination, kinship and sample identity controls
- Annotate variants from more than fifty public sources, plus CKB Boost and COSMIC as premium options
- Compute oncology signatures including MSI, TMB, clonality and HRD status
- Produce, sign off and export a clinical report, in QC, VKB or JSON formats
- Automate the whole pipeline with SeqOne Flow, from file transfer to analysis launch, connected to the laboratory's LIMS
When to use SeqOne Platform / When not to
A quick filter to help you decide if SeqOne Platform is the right fit.
When to use SeqOne Platform
- Clinical molecular laboratories running routine NGS diagnostics who need software that is itself a regulated in vitro diagnostic device
- Bioinformaticians and clinical geneticists who want variant prioritisation they can audit, with an explainable score rather than a black box
- Laboratories running germline and somatic work side by side, on panels, exomes and genomes, with short-read and long-read chemistries
- Laboratory managers looking to automate the hand-offs between sequencer, LIMS and reporting instead of moving files by hand
- Teams migrating away from Agilent Alissa or Cartagenia, for whom the publisher documents a dedicated transition path
When not to use SeqOne Platform
- Individuals and patients: this is a business-to-business tool sold to laboratories, with no consumer offering and no direct patient access
- Anyone who needs a published price before talking to a salesperson, since all four plans are quoted
- Organisations that need a permanent free tier, as the only free access is a 30-day trial
- Teams without their own sequencing capability, since the terms of use place sequencing squarely under the customer's sole responsibility
- Users expecting a mobile app or a self-service API integration, as neither a mobile application nor public API documentation exists
How to use SeqOne Platform
A typical end-to-end flow, from setup to results.
- Request a 30-day free trial from the sign-up page, or book a demonstration if you prefer a guided walkthrough
- Choose your regional instance at login, from Europe, the United States, Australia, Switzerland, the United Kingdom or Canada
- Agree the scope with sales, since the four plans and every custom deployment option are quoted individually
- Import your sequencing data, in panels, exomes or genomes, from short-read or long-read runs
- Let the automated quality checks clear coverage, contamination, kinship and sample identity before interpretation
- Configure a workset to designate the content to analyse and the algorithmic approach to apply
- Review the DiagAI-ranked shortlist and the annotations, and classify the variants that matter
- Produce the clinical report and export the results in QC, VKB or JSON format
- Connect SeqOne Flow to your sequencer and LIMS to automate the whole sequence, using API, file or e-mail triggers
- Use the two annual training sessions and tiered level 1 to 3 support to onboard the rest of the team
Pros & Cons
Pros
- An unusually strong regulatory position for software: CE-IVD Class C under the IVDR, plus ISO 13485, ISO 27001 and HDS, with the certificates downloadable from a public trust centre
- DiagAI performance is published and peer-reviewed, with named cohorts including 565 Genomics England whole-genome cases and more than 65,000 ClinVar structural variants
- Genuinely sequencer agnostic, with short-read and long-read support and named partnerships with Oxford Nanopore Technologies and MGI Tech
- A 30-day free trial run on the laboratory's own samples, with expert support and no commitment
- Unlimited user seats in all four plans, which is uncommon in clinical software
- Consumption-based billing announced without volume constraints or hidden fees, alongside a documented HDS commitment that health data does not leave the European Economic Area
- A documented migration path for laboratories leaving Agilent Alissa or Cartagenia
Cons
- No price is public anywhere: all four plans route to a sales conversation, so no comparison is possible before a quotation
- No permanent free plan; free access is capped at 30 days
- The terms of use let SeqOne reuse anonymised uploaded material to improve its algorithms, and no opt-out is documented
- A public API is sold in every plan, yet no public API documentation exists and the support knowledge base sits behind a SAML login
- The platform terms of use are linked neither from the navigation nor from the sitemap, so a prospect can easily miss them
- No hosting country is ever named; only a regional European Economic Area commitment covering personal health data
- The heaviest capabilities, namely virtual private cloud, on-premise, LIMS and EHR, are all quoted as custom, and HRD status carries an extra per-analysis charge
Pricing & Plans
No price is published. The pricing page presents four plans, Germline, Germline Tertiary, Somatic and Somatic Tertiary, and each routes to a Talk to sales button, so every figure is quoted individually. The stated commercial model is consumption-based: SeqOne advertises transparent per-sample pricing and pay-per-analysis billing with no volume constraint and no long-term commitment. A 30-day free trial run on the customer's own samples is offered, but there is no permanent free plan. Two paid extensions are flagged on the same page: HRD status carries an extra price per analysis and is limited to specific applications, while GenomeAlert! and SeqOne Flow Cloud sit in a Premium Pack. Virtual private cloud, on-premise, LIMS installation and EHR integration are all marked as custom.
- germline secondary and tertiary analysis on panels
- with quality control
- ACMG
- REVEL
- CI-SpliceAI and AlphaMissense classifications and annotation from more than fifty public sources. Price on quotation.
- germline tertiary interpretation
- extending coverage to whole exome and whole genome analysis. Price on quotation.
- oncology plan adding AMP Tier oncogenicity classification
- CKB Boost and COSMIC premium annotation
- and MSI
- TMB and clonality signatures. Price on quotation.
- somatic tertiary interpretation with the same premium annotation sources and genomic signature coverage. Price on quotation.
- HRD status at an extra price per analysis
- GenomeAlert! and SeqOne Flow Cloud as a Premium Pack
- and virtual private cloud
- on-premise
- LIMS installation and EHR integration quoted as custom.
Data, GDPR & hosting
A consolidated view of how SeqOne Platform handles your data.
GDPR overview
GDPR implementation is documented in concrete terms. The privacy notice, last updated 8 December 2025, names SeqOne S.A.S. as primary controller and covers the services formerly sold as Life&Soft and Congenica. It cites the EU GDPR, the UK GDPR under the DPA 2018 and HIPAA for United States activity, sets out a lawful basis for each processing activity, relying on Article 9(2)(h) and Article 6(1)(f) for genomic and health data, and lists the eight data subject rights. A data protection officer answers at dpo@seqone.com and by post in Montpellier, and a data protection representative is designated in Cambridge for the United Kingdom. Complaints route to the CNIL, the ICO or the HHS Office for Civil Rights. Transfers outside the EU and UK rely on standard contractual clauses and binding corporate rules. The trust centre marks GDPR and UK GDPR as compliant, with ISO 27701 still in progress.
Who owns the data?
SeqOne states on its homepage that customer data stays yours, never shared and never sold, and that each patient file is secured by a patented double-encryption scheme with its own key. The platform terms of use keep intellectual property in the software itself with SeqOne: subscribing grants the client no ownership over the publisher's platform or assets. For patient data the privacy notice places SeqOne in the role of processor under the GDPR and UK GDPR, or business associate under HIPAA, acting on the instructions of the client laboratory. That laboratory remains the controller and is responsible for securing the lawful basis before any patient data is transferred.
Reuse rights
Article 9 of the platform terms of use gives SeqOne a right of access to the material uploaded by users, for the stated purpose of improving the platform and its algorithms for the benefit of all clients: the text names SeqOneRank, ACMG classification, variant viewer filter modules, bug fixing and pipeline updates. For those purposes only, SeqOne may reuse uploaded material after anonymising it, with FASTQ files excluded and deleted instead. No opt-out mechanism is documented anywhere on the site. On the customer side, clients can export their own analysis files in QC, VKB and JSON formats and reuse their results, but the terms grant no right to reproduce, adapt or commercially exploit the platform or its components.
Data retention & training
Hosting summary
The trust centre publishes a single subprocessor for the platform: AWS, listed as a cloud provider. A separate French-language regulatory page carries the detail that matters. SeqOne is itself certified as a health data host under the French HDS scheme, with Amazon (AWS) as an HDS-certified subprocessor, and it commits that no personal health data is transferred to a country outside the European Economic Area. The same table answers HDS requirements 29 and 30 in the negative: no access to health data from outside the EEA, and no exposure to a third-country law that would compel such access. Neither party is qualified SecNumCloud 3.2. The privacy notice describes hosting providers only as ISO 27001 and HDS certified hosts. No hosting country is ever named. Note that the platform is also offered through regional instances for the United States, Australia, Canada, Switzerland and the United Kingdom, including a HIPAA-compliant US platform, so the EEA commitment cannot cover every deployment. The marketing website itself is hosted by Webflow.
Things to keep in mind
Risks and trade-offs to weigh before adopting SeqOne Platform.
- The homepage promises that your data stays yours and is never shared, while article 9 of the platform terms of use reserves a right to reuse anonymised uploaded material to improve SeqOne's algorithms. Read both before signing.
- No training opt-out is documented anywhere, so the reuse clause has to be negotiated in the data processing agreement rather than toggled in a setting.
- The terms of use are reachable neither from the site navigation nor from the sitemap; a laboratory can contract without ever having seen them.
- The European Economic Area hosting commitment covers personal health data under the HDS scheme, but the platform is also offered through United States, Australian, Canadian, Swiss and British instances that fall outside that perimeter by construction.
- An explainable score is still a score: DiagAI ranks candidates and the publisher stresses human oversight, so the risk is a team that stops looking past the shortlist.
- Accreditations named in the case studies, such as those of partner hospitals and reference laboratories, belong to those customers and not to SeqOne; do not read them as guarantees from the publisher.
- CE-IVD coverage applies to the platform, but not every module is treated alike, since HRD status is explicitly limited to specific applications and billed separately.
Setup & Integrations
Technical difficulty
Getting started is light: create an account, pick your regional instance and run the 30-day trial in a browser with your own samples, with expert support included. Clinical use is heavier. Laboratories are expected to validate the workflow on their own data, and the demanding parts, namely SeqOne Flow connections to the sequencer and LIMS, EHR integration and virtual private cloud or on-premise installation, are all quoted as custom projects. Two training sessions a year and tiered level 1 to 3 support are included. Sequencing itself remains the customer's responsibility.
Deployment
Integrations
Behind SeqOne Platform
Fundraising
Resources
All the official URLs gathered for verification and reference.
Alternatives
Tools that compete with or complement SeqOne Platform.
Frequently asked questions
Is SeqOne Platform a regulated medical device?
How much does SeqOne Platform cost?
Is there a free trial or a free plan?
Does SeqOne Platform have an API?
Where is the data hosted?
Is my laboratory data used to train the algorithms?
Can the platform be installed on our own infrastructure?
Can we migrate from another interpretation platform?
Who publishes SeqOne Platform?
Should you pick SeqOne Platform?
SeqOne Platform is one of the few genomic interpretation tools that carries the regulatory weight its market demands. Being a CE-IVD Class C device under the IVDR, backed by ISO 13485, ISO 27001 and HDS certification with downloadable certificates on a public trust centre, is not marketing polish: it is what lets a laboratory put the software in a clinical workflow without building the compliance case itself. The DiagAI engine is the other serious argument, and unusually for this field its performance is published and peer-reviewed against named cohorts rather than asserted.
The reservations are commercial and contractual rather than technical. Nothing about the price is public. Four plans all end at the same Talk to sales button, the heaviest deployments are quoted as custom, and HRD status carries a surcharge, so budgeting requires a conversation. A public API is sold in every plan but has no public documentation, which is an odd gap for a product built on integration. And the platform terms of use, which sit outside the navigation and outside the sitemap, reserve to SeqOne a right to reuse anonymised uploaded material to improve its algorithms, with no documented opt-out. That is a defensible clause for a diagnostic platform that improves through use, but it deserves to be read next to the homepage promise that your data is never shared, and negotiated in the data processing agreement.
For a molecular laboratory already running routine NGS, the sensible route is the 30-day trial on your own samples, with two questions prepared for the sales call: the exact scope of the API, and whether the reuse clause can be narrowed contractually. For anyone outside that profile, this is not a tool to evaluate casually.
- Choosing a selection results in a full page refresh.
- Opens in a new window.