Basepair

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.

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

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

• Genomics analysis software
• NGS data analysis
• Bioinformatics platform
• Cloud bioinformatics services
• Multi-omics data analysis

Headquarters

HQ city

New York

HQ country

United States

HQ region

North America

Offices1 record

Markets served

GTM type

B2B

Offering type

Software

Cost components

Technology or R&D, Personnel, Marketing or Sales, Infrastructure, Operations

Revenue model

1. 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.
2. 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.
3. 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.
4. 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.
5. 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

Go-to-market motion5 records

Distribution channels7 records

Marketing channels7 records

Core 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

Named customers13 records

Segments5 records

Ideal customer profiles3 records

Technology focussed Yes

API detail

Has API

Yes

API docs

API detail

Core technology

AI maturity

App detail

Integration4 records

AI capability6 records

Feature10 records

Partnerships

Twelve partnerships are on record, tiered core and minor.

• NalaGeneticscoreStrategic or Co-development Partner · 29 October 2025Launch 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 ChemicalsminorChannel Partner/ Reseller/ Distributor · 14 May 2025Partnership to bring scalable, cloud-based genomic analysis to Japan, empowering Japanese researchers with end-to-end genomic solutions.
• TrendBiocoreChannel Partner/ Reseller/ Distributor · 11 February 2025Distribution agreement to enhance genomic research in Australia & New Zealand, democratizing access to advanced genomic analysis tools in the region.
• SciencewerkecoreChannel Partner/ Reseller/ Distributor · 24 January 2025Distribution agreement to bring cutting-edge bioinformatics solutions to Southeast Asia, accelerating genomic research and precision medicine initiatives across the region.
• NVIDIAcoreTechnology or Integration · 6 November 2024Strategic 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)coreTechnology or Integration · 22 May 2024Deep 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 MedicalcoreTechnology or Integration · 15 February 2024Strategic 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 or Integration · 2 November 2023Technology 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.
• AstridecoreChannel Partner/ Reseller/ Distributor · 11 September 2023Distribution 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 BiosciencescoreTechnology or Integration · 21 August 2023Collaboration 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 GenomicscoreTechnology or Integration · 3 November 2022Partnership 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 BiocenterminorChannel Partner/ Reseller/ Distributor · 13 September 2018Partnership 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

Direct 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

• Xx.com/basepairtech
• YouTubeyoutube.com/channel/UCU9e71npC28kI4diR8Azz6Q
• Facebookfacebook.com/BasepairTech
• LinkedInlinkedin.com/company/basepair

Revenue estimate

Valuation estimate

Number of profiles

Profiles4 records

Funding overview

Funding rounds9 records

Investors7 records

Funding detail is available on the Subscription and Enterprise plan.Contact sales →

M&A

Investments

M&A and investment is available on the Subscription and Enterprise plan.Contact sales →

Frequently asked questions about Basepair