Basepair
Basepair is a cloud-native SaaS platform providing point-and-click bioinformatics analysis for next-generation sequencing data, with a federated architecture that provisions inside customers' own AWS accounts. It serves academic researchers, biopharma R&D teams, diagnostic kit manufacturers, and clinical laboratories with 50+ automated genomics, transcriptomics, and epigenomics workflows.
- Company typePrivate
- Founded2018
- HeadquartersNew York, United States
- Headcount1–10
- GTM typeB2B
- OfferingSoftware
What Basepair does
Basepair is a cloud-native SaaS platform that provides point-and-click bioinformatics analysis for next-generation sequencing (NGS) data. Founded in 2017-2018 by Amit Sinha, PhD, while at Harvard Medical School, the company targets bottlenecks in genomic data analysis that traditionally require specialized bioinformatics expertise. Its core differentiation is a federated analytics architecture that provisions inside customers' own AWS accounts for both storage and compute—the company claims it is the first and only SaaS platform with this capability—eliminating data movement, enhancing security, and reducing cloud costs by up to 80% on storage.
The platform offers over 50 automated workflows spanning genomics (DNA-Seq, whole genome/exome, targeted panels, CRISPR, Hi-C), transcriptomics (RNA-Seq, single-cell RNA-Seq), and epigenomics (ChIP-Seq, ATAC-Seq, CUT&RUN, CUT&TAG). Key technology integrations include NVIDIA Parabricks for GPU-accelerated analysis (up to 108x faster than CPU solutions), AWS HealthOmics for enterprise-scale workflow execution, and seamless data import from Illumina BaseSpace, NCBI GEO/SRA, and FTP/SFTP. The platform supports white-labeled web portals for kit/assay manufacturers and distributors, plus Python and command-line APIs for programmatic automation.
Basepair operates a multi-channel go-to-market combining product-led growth (freemium with 6 free samples, self-serve signup), enterprise field sales (annual unlimited licenses, custom workflows), AWS Marketplace distribution, and a growing network of regional channel partners across Japan, Australia/New Zealand, and Southeast Asia. Revenue streams include usage-based per-sample fees, annual subscription licenses, white-label portal licensing, and marketplace transactions. The company serves academic research institutions (Harvard, Yale, Stanford, NIH), healthcare providers (Memorial Sloan Kettering, NYU Langone, RMA of NY), biotechnology companies (Scale Biosciences, NKarta, Complete Genomics), and diagnostic test manufacturers across North America, Europe, and Asia-Pacific.
Basepair firmographics
Firmographics- Name
- Basepair
- Legal name
- Basepair Inc.
- Website
- https://basepairtech.com
- Company type
- Private
- Founded year
- 2018
- Operating status
- Operating
- Headcount range
- 1–10 employees
- Short description
- Basepair is a cloud-native SaaS platform providing point-and-click bioinformatics analysis for next-generation sequencing data, with a federated architecture that provisions inside customers' own AWS accounts. It serves academic researchers, biopharma R&D teams, diagnostic kit manufacturers, and clinical laboratories with 50+ automated genomics, transcriptomics, and epigenomics workflows.
- Ownership category
- akta.pro rank
Basepair industry classification
Industry- Product category
- Bioinformatics Software
- NAICS
- Software Publishers (513210)
- SIC
- Services-Prepackaged Software (7372), Services-Computer Programming, Data Processing, Etc. (7370)
- akta.pro primary industry
- Genomics & Next-Generation Sequencing (NGS) Services (HLAGANAA)
- akta.pro secondary industry
- Enterprise PaaS (App Runtime & Managed Application Platforms) (HDAEAKAB)
Keywords
Where Basepair is headquartered
LocationHeadquarters
- HQ city
- New York
- HQ country
- United States
- HQ region
- North America
Offices1 record
Markets served
Basepair business model
Business model- GTM type
- B2B
- Offering type
- Software
- Cost components
- Technology or R&D, Personnel, Marketing or Sales, Infrastructure, Operations
Revenue model
- Per-Sample Usage Fees: Pay-as-you-go per sample pricing model that includes all analysis, annual storage, and software usage fees. Customers can start small and scale usage without upfront costs.
- Annual Unlimited Licenses: Unlimited annual licenses for large-scale initiatives at a set price, providing cost-effective pricing as analysis volumes grow with predictable budgeting.
- AWS Marketplace Transactions: Platform available through AWS Marketplace with simplified pay-as-you-go licensing, enabling customers to use existing AWS commitments and discount plans.
- White Label/Portal Licensing: Partners and distributors can white-label the platform and offer their own versions through coupon-based business operations, generating recurring licensing revenue.
- Freemium Trial: Free tier offering 6 samples for free with unlimited analyses, designed to convert users to paid plans as their needs grow.
Pricing tiers
| Model | Billing | Price |
|---|---|---|
| Usage-based | Pay-as-you-go | Pay-as-you-go per sample model |
| Subscription | Annual | Annual unlimited license |
| Usage-based | Pay-as-you-go | AWS Marketplace pricing |
| Freemium | Pay-as-you-go | Free trial tier |
Go-to-market motion5 records
Distribution channels7 records
Marketing channels7 records
Basepair product offering
Product offeringCore offering
Basepair is a SaaS bioinformatics platform that enables point-and-click next-generation sequencing (NGS) data analysis. The platform provisions within customers' own AWS accounts for both storage and compute, eliminating genomic data movement while supporting over 50 automated pipelines for genomics, transcriptomics, and epigenomics. It also offers white-labeled web portals, GPU-accelerated analysis via NVIDIA Parabricks, and co-developed clinical applications such as PaRTI-Cular and Nala Basecamp.
Product overview
Basepair is a market-leading point-and-click bioinformatics SaaS platform for NGS data analysis. The core Basepair Platform provisions within customers' own AWS accounts for both storage and compute, eliminating data movement while enhancing security and reducing costs. The platform offers over 50 automated workflows for genomics (DNA-Seq, whole genome, exome, targeted panels, CRISPR, Hi-C), transcriptomics (RNA-Seq, single cell RNA-Seq), and epigenomics (ChIP-Seq, ATAC-Seq, CUT&RUN, CUT&TAG). Additional offerings include White Labeled Web Portals for distributors and kit manufacturers, NVIDIA Parabricks Integration for GPU-accelerated analysis (up to 108x faster), AWS HealthOmics Integration for enterprise-scale workflows, Custom Workflow Solutions using Nextflow/WDL/Docker, Nala Basecamp for clinical genomics with NalaGenetics, and PaRTI-Cular for infectious disease testing with Micronbrane Medical. The platform democratizes NGS analysis by enabling bench scientists to run analyses with point-and-click interfaces while providing APIs and CLI for bioinformaticians.
Differentiator
Problem solved
Functional benefit
Products and services
- Basepair Platform Cloud-native SaaS platform providing point-and-click bioinformatics for NGS data analysis. Provisions within customers' own AWS accounts for both storage and compute, eliminating data movement and enhancing security. Offers over 50 automated workflows for genomics, transcriptomics, and epigenomics analysis with interactive visualizations.
- White Labeled Web Portals Deploy workflows to end users via white labeled web portals in weeks. Create unique coupon codes to bundle the right amount of analysis at the point of sale of kits, assays, or diagnostic tests. Keeps customers within the distributor's own brand and ecosystem.
- PaRTI-Cular Pathogen Real-Time Identification web application for metagenomic NGS analysis. Developed with Micronbrane Medical for rapid infectious disease testing. Produces results in 30 minutes from sequenced samples with database benchmarking for thousands of microorganisms.
- Nala Basecamp Collaborative clinical genomics platform integrating pharmacogenomics and polygenic risk scores. Joint platform with NalaGenetics featuring cloud-native, regulatory-compliant bioinformatics for clinical workflows.
Quantifiable outcome
- Analysis time reduced from days/weeks to under an hour for multiple samples
- +4 more outcomes
Companies that use Basepair
Customer profileNamed customers13 records
Segments5 records
Ideal customer profiles3 records
Basepair technology and API
TechnologyTechnology focussed Yes
API detail
- Has API
- Yes
- API docs
- API detail
Core technology
AI maturity
App detail
Integration4 records
AI capability6 records
Feature10 records
Basepair partnerships and signals
Strategic signalPartnerships
Twelve partnerships are on record, tiered core and minor.
- NalaGeneticscoreLaunch of Nala Basecamp collaborative platform integrating clinical genomics with advanced data analysis for pharmacogenomics and polygenic risk scores, leveraging cloud-native regulatory-compliant bioinformatics.
- IWAI ChemicalsminorPartnership to bring scalable, cloud-based genomic analysis to Japan, empowering Japanese researchers with end-to-end genomic solutions.
- TrendBiocoreDistribution agreement to enhance genomic research in Australia & New Zealand, democratizing access to advanced genomic analysis tools in the region.
- SciencewerkecoreDistribution agreement to bring cutting-edge bioinformatics solutions to Southeast Asia, accelerating genomic research and precision medicine initiatives across the region.
- NVIDIAcoreStrategic collaboration to integrate NVIDIA Parabricks GPU-accelerated genomic analysis tools into Basepair's platform, providing up to 108x faster performance for genomic data analysis while maintaining Basepair's intuitive point-and-click interface.
- Amazon Web Services (AWS)coreDeep integration with AWS HealthOmics service and broader AWS platform, enabling customers to leverage AWS compute and storage resources in their own accounts. Basepair is an AWS Partner with qualified software status.
- Micronbrane MedicalcoreStrategic partnership to power PaRTI-Cular Web App for rapid infectious disease testing through metagenomic NGS. Basepair enables secure cloud deployment in customer AWS accounts, reducing security risks and streamlining mNGS analysis.
- Complete GenomicscoreTechnology integration partnership enabling Complete Genomics customers to seamlessly access Basepair's bioinformatics platform on AWS, either provisioning in their own accounts or via Basepair's hosted service, with preferential commercial terms.
- AstridecoreDistribution agreement for Japan market, enabling Astride to offer Basepair's platform with white-labeling and coupon-based business operations to Japanese researchers, addressing data sovereignty concerns.
- Scale BiosciencescoreCollaboration to provide point-and-click bioinformatic analysis of single-cell data produced with Scale Biosciences' combinatorial indexing technology, enabling customers to quickly adopt single-cell protocols without in-house bioinformatics capabilities.
- Arima GenomicscorePartnership to make Arima Genomics' bioinformatics pipelines (including Arima-SV) accessible through Basepair's user-friendly interface, decreasing compute time and generating easy-to-understand reports for 3D genomics data.
- TATAA BiocenterminorPartnership to offer faster NGS data analysis through integrated online portal and use in NGS training courses, serving TATAA's customers in Europe.
Scale indicators6 records
Recent moves6 records
Expansion highlights6 records
Basepair competitors and assessment
Company assessmentDirect peers
- DNAnexus: Cloud-based genomics and biomedical informatics platform serving pharma, biotech, and clinical customers. Most direct comparison to Basepair: managed NGS analysis pipelines, federated/cloud architecture, and enterprise SaaS model.
- Velsera (formerly Seven Bridges Genomics): Genomics analysis platform providing a federated, cloud-based environment for NGS and multi-omics workflows. Overlaps directly with Basepair on cloud-native bioinformatics for research and clinical customers.
- Terra.bio (Broad Institute / Verily): Cloud-based genomics and biomedical research platform built on Microsoft Azure/Google Cloud with WDL workflow support. Directly comparable cloud bioinformatics offering with strong academic adoption, especially in the same Harvard/Broad/MSKCC customer set Basepair targets.
- Lifebit Biotech: Cloud-native genomics platform offering federated analytics for biomedical and clinical data. Directly comparable on federated architecture and enterprise positioning, particularly with pharma and public-sector genomics customers.
- Genestack: Cloud-based omics data management and analysis platform used by pharma and research institutions. Comparable on multi-omics analysis, federated data access, and enterprise GTM.
- BlueBee: Cloud genomics analysis platform focused on regulated, secure NGS data processing for clinical and research customers. Comparable on cloud-native architecture and emphasis on data governance/security.
Broad incumbents
- Illumina BaseSpace Sequence Hub: Illumina's cloud-based NGS analysis ecosystem tightly coupled with its sequencers. Competes with Basepair in the same NGS analysis space but bundles hardware, reagents, and software as a vertically integrated incumbent.
- QIAGEN Digital Insights: QIAGEN's bioinformatics portfolio including QIAseq and CLC Genomics, offering NGS analysis for research and clinical diagnostics. Competes with Basepair at the bioinformatics layer but as part of a much larger life sciences portfolio with established clinical and IVD sales channels.
Emerging players
- Form Bio (DNA Script): Bioinformatics platform providing NGS data analysis, workflow management, and storage for researchers. Closely comparable on cloud-hosted NGS pipelines and developer/biologist workflows.
Others
- Arima Genomics: 3D genomics technology provider and Basepair partner. Comparable not as a direct competitor but as a sequencing-technology partner whose pipelines run on Basepair, illustrating the partner/kit-manufacturer layer that white-label portals target.
Market position
Strengths5 records
Weaknesses5 records
Competitive moat6 records
Key risks6 records
Key highlights7 records
Customer concentration
Basepair social profiles
Digital presenceBasepair financial estimates
Financial estimateRevenue estimate
Valuation estimate
Basepair leadership team
Management profileNumber of profiles
Profiles4 records
Basepair funding detail
Funding detailFunding overview
Funding rounds9 records
Investors7 records
Funding detail is available on the Subscription and Enterprise plan.Contact sales →
Basepair M&A and investment
M&A and investmentM&A
Investments
M&A and investment is available on the Subscription and Enterprise plan.Contact sales →
Frequently asked questions about Basepair
What does Basepair do?
Basepair is a SaaS bioinformatics platform that enables point-and-click next-generation sequencing (NGS) data analysis. The platform provisions within customers' own AWS accounts for both storage and compute, eliminating genomic data movement while supporting over 50 automated pipelines for genomics, transcriptomics, and epigenomics. It also offers white-labeled web portals, GPU-accelerated analysis via NVIDIA Parabricks, and co-developed clinical applications such as PaRTI-Cular and Nala Basecamp.
Is Basepair a public or private company?
Basepair is a private company. It is classified as venture growth investor backed and is currently operating.
When was Basepair founded?
Basepair was founded in 2018. It employs 1 to 10 people.
Where is Basepair based?
Basepair is headquartered in New York, United States, in the North America region.
How does Basepair make money?
Five revenue lines are on record. Per-Sample Usage Fees are the primary driver. The others are annual Unlimited Licenses, AWS Marketplace Transactions, white Label/Portal Licensing and freemium Trial.
Who are Basepair's main competitors?
Direct peers on record are DNAnexus, Velsera (formerly Seven Bridges Genomics), Terra.bio (Broad Institute / Verily), Lifebit Biotech, Genestack and BlueBee. Broad incumbents are Illumina BaseSpace Sequence Hub and QIAGEN Digital Insights. Form Bio (DNA Script) is listed as an emerging player. Arima Genomics is listed as an others.
Does Basepair have an API?
Yes. Basepair provides a powerful Application Programming Interface (API) for Python and command line. The API enables automation of NGS data analysis at scale, allowing users to programmatically upload samples, trigger analyses, and retrieve results. With the API, users can process dozens, hundreds, or thousands of samples efficiently. Basepair has over 50 workflows and counting that can be executed via the API. Developer documentation is at support.basepairtech.com/support/solutions/folders/14000121460.
What industry is Basepair in?
Basepair's product category is Bioinformatics Software. Its primary akta.pro industry code is HLAGANAA, Genomics & Next-Generation Sequencing (NGS) Services, with a secondary code of HDAEAKAB, Enterprise PaaS (App Runtime & Managed Application Platforms). Its NAICS code is 513210 and its SIC code is 7372.