NGS Data Analysis Platform

Basepair NGS Data Analysis Platform is a Software-as-a-Service (SaaS) bioinformatics solution designed for academic, commercial, and clinical research teams working with next-generation sequencing (NGS) data. Unlike traditional hosted platforms, Basepair is uniquely capable of provisioning directly within a customer's own AWS account, eliminating the need to move genomic data to an external environment. This approach enhances data security, reduces cloud costs, and allows organizations to maintain full control over their data governance and usage commitments.

Basepair serves a broad range of users — from bench scientists who prefer a point-and-click graphical interface to experienced bioinformaticians who require CLI and API access. The platform democratizes NGS data analysis by reducing bottlenecks between wet and dry lab teams, accelerating time to scientific and diagnostic insight, and freeing bioinformatics teams to focus on complex problems rather than routine analyses.

Key Differentiators

• No data movement required: Connect your own AWS account to leverage existing compute and storage investments without uploading data to a hosted solution, eliminating data duplication and reducing IT costs.
• Easy to use for everyone: A point-and-click interface for scientists at the bench, alongside CLI and API access for bioinformaticians.
• Interactive visualization: Dynamic, parameter-driven visualizations replace static HTML pages and flat files, allowing users to explore data in real time.
• Customized white-label web portals: 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.
• Flexible, cost-effective pricing: Options range from pay-as-you-go per sample for smaller projects to unlimited annual licenses for large-scale initiatives, with discounts available through the AWS Marketplace.

Platform Capabilities

• Streamlined data import: Seamlessly import data from BaseSpace, NCBI GEO/SRA, and FTP/SFTP directly within the platform, ensuring efficient data transfer without leaving the Basepair environment.
• Custom workflow solutions: Deploy personalized workflows tailored to specific research needs, supporting automation of data analysis, task streamlining, and resource optimization.
• Integrated MultiOmics via AWS HealthOmics: Access advanced HealthOmics capabilities through an intuitive interface, enabling users to benefit immediately without significant implementation effort or training.
• Advanced data storage management: Save up to 80% on monthly storage costs through fine-grain control over data archival and dynamic retrieval, outperforming S3 intelligent tiering. Large omics files such as FASTQ and BAM are automatically moved to cold storage after analysis and seamlessly un-archived when re-analysis is needed.
• Security and access control: The platform adheres to industry security standards, using HTTPS exclusively for all web interface and API communications. Users have complete control over who can access their data, with permissions explicitly granted on a per-user basis.

Out-of-the-Box Automated Pipelines

Basepair provides industry-standard, automated pipelines for a wide range of NGS data types, as well as support for custom workflows:

• Genomics: Whole Genome, Whole Exome, Targeted Panels, CRISPR, Hi-C
• Transcriptomics: RNA-Seq, Single Cell RNA-Seq
• Epigenomics: ATAC-Seq, ChIP-Seq, SNAP-ChIP, CUT&RUN, CUT&TAG
• Custom / Home Brew workflows: Support for Nextflow, WDL, YAML, Docker, GitHub, and ECR

Integrations and Partnerships

• Powered by AWS HealthOmics for advanced genomic pipeline execution
• GPU-accelerated analysis through integration with NVIDIA Parabricks
• Strategic partnerships with Novocraft, Micronbrane Medical, IWAI Chemicals, TrendBio, and Sciencewerke to extend cloud-based genomic analysis across global markets including Japan, Australia, New Zealand, and Southeast Asia

Basepair's work has been cited in dozens of peer-reviewed journals and is trusted by researchers at leading institutions including Yale University and NYU Langone Health. The platform is suitable for federated deployment scenarios where data residency, security, and cost efficiency are critical priorities, and it supports both individual research projects and enterprise-scale genomic programs.