Basepair

Basepair is a Software-as-a-Service (SaaS) next-generation sequencing (NGS) data analysis platform designed to make bioinformatics accessible, efficient, and secure for academic, commercial, and clinical research organizations. Founded by Harvard Medical School computational biologist Amit Sinha, PhD, Basepair was built on the belief that all scientists — from bioinformaticians to bench biologists — should be able to analyze, visualize, and interpret genomic data without barriers. The platform is uniquely architected to provision directly within a customer's own AWS account, eliminating the need to move genomic data to a hosted solution, enhancing data governance and security, and reducing cloud infrastructure costs.

Basepair addresses a critical challenge in modern genomics: as NGS technology generates data at unprecedented scale, the bottleneck has shifted from data generation and processing to who can perform analysis and understand the results. By democratizing access to genomic analysis through an intuitive GUI-driven experience alongside CLI and API access, Basepair reduces inefficiencies in R&D teams, shortens time to market for assay manufacturers, and improves turnaround times in clinical settings. The platform has earned the trust of industry leaders and has developed strategic partnerships with major organizations including Amazon Web Services (AWS) and Complete Genomics.

Core Platform Capabilities

• No data movement required: Customers connect their own AWS account to leverage existing compute and storage investments, eliminating data duplication, enhancing security, and reducing IT costs without technical lock-in.
• Dual-mode interface: A point-and-click GUI empowers bench scientists to run analyses independently, while CLI and API access gives bioinformaticians full programmatic control.
• Interactive data visualization: Dynamic, parameter-driven visualizations replace static flat files and HTML reports, enabling researchers to explore and interrogate their data in real time.
• Custom workflow deployment: Users can build and deploy their own tailored workflows to automate data analysis, streamline tasks, and optimize resource utilization according to their specific research needs.
• Customized white-label web portals: Organizations can deploy workflows to end users via branded web portals within weeks, with support for unique coupon codes to bundle analysis at the point of sale of a kit, assay, or diagnostic test.
• Integrated MultiOmics solutions: The platform supports comprehensive AWS HealthOmics analysis to enhance data insights and research outcomes.
• GPU-accelerated analysis: Basepair accelerates genomic data analysis using NVIDIA Parabricks, enabling faster processing of high-throughput sequencing data.

Data Management and Storage

• Advanced storage management: Customers can save up to 80% on monthly storage costs through fine-grain control over data archival and dynamic retrieval, outperforming AWS S3 intelligent tiering.
• Streamlined data import: Seamless integration with BaseSpace, NCBI GEO/SRA, and FTP/SFTP allows users to import data from diverse sources without leaving the Basepair platform, ensuring efficient data transfer and saving time.
• Federated architecture: By provisioning within a customer's own AWS account, Basepair ensures data remains in place, supporting data governance requirements and leveraging existing cloud commitments and economies of scale.

Security and Compliance

• The platform adheres to industry security standards, with all web interface and API communications exclusively using HTTPS to encrypt data in transit.
• Customers maintain full control over their data governance, security policies, and cloud usage commitments by operating within their own AWS environment.
• Eliminating data movement to third-party hosted environments reduces exposure and ensures zero unnecessary data duplication.

Pricing and Deployment Models

• Flexible pricing options include pay-as-you-go per sample for smaller projects and unlimited annual licenses for large-scale initiatives.
• Discounts are available for orders placed through the AWS Marketplace.
• A cloud storage savings estimator is available to help organizations calculate potential cost reductions.
• The platform is also available in a version powered by AWS HealthOmics for organizations requiring that infrastructure.

Global Partnerships and Ecosystem

• Basepair has partnered with Micronbrane Medical to streamline metagenomic NGS (mNGS) analysis on AWS.
• A partnership with IWAI Chemicals brings scalable, cloud-based genomic analysis to Japan.
• A strategic partnership with Novocraft delivers advanced genomic pipelines in the cloud.
• Distribution agreements with TrendBio and Sciencewerke extend Basepair's reach into Australia, New Zealand, and Southeast Asia.
• The platform is trusted by industry leaders and backed by the broader AWS partner ecosystem.

Leadership and Team

• Amit Sinha, PhD (CEO & Founder): Computational biologist with a decade of expertise, formerly an Instructor at Harvard Medical School.
• Simon Valentine (Chief Commercial Officer): Over 25 years of commercial leadership in scientific software, including roles leading global enterprise informatics sales at Illumina and VP of North America Sales at Seven Bridges Genomics.
• Blas Vicco (Director of Engineering): Computer engineer with over 15 years of experience in web application development.
• Luke Wojenski (Senior Bioinformatics Scientist): PhD in genetics and genomics with research focused on transcription regulation during human cell division and NGS-based biological analysis.
• Priyanka Mulay (Product Manager): Certified Scrum Product Owner with a master's in Biotechnology, over a decade of experience in clinical reporting, precision medicine, oncology, and genetics, and leadership of COVID-19 sequencing surveillance studies in Southern India.
• Suman Chakraborty (Executive Director, Global Business Development): Experienced SaaS and life sciences business development leader driving international growth, strategic partnerships, and market expansion for Basepair.
• Siddhant Rathore (Bioinformatics Engineer): Trained bioinformatician and data scientist specializing in the development and optimization of end-to-end pipelines for high-throughput sequencing data.

Basepair is committed to the vision that precision medicine requires a platform that democratizes genomic data analysis while keeping data secure, costs manageable, and workflows accessible to scientists of all technical backgrounds. By combining a federated cloud architecture, intuitive interfaces, and a growing global partner network, Basepair enables research, commercial, and clinical organizations to accelerate time to scientific and diagnostic insight.