NGS Analysis, Delivered Made Simple Accelerated Federated
Bioinformatics in the cloud should be easier. Basepair is the first and only Software-as-a-Service (SaaS) platform that can provision in your own AWS account for both storage and compute, eliminating genomic data movement, enhancing security and reducing costs.

Trusted by Industry Leaders at

As more healthcare and life science information moves to the cloud, a growing need is to create an environment where research scientists can execute their workflows and interactively visualize their data. 

Basepair helps bring a simplified GUI-driven experience to make it easier for scientists to execute their research. 

Moreover, this execution is done within a customer’s own AWS account, allowing them to maintain control of their data governance, security, and usage commitments.

Tehsin Syed

General Manager of Health AI Services, AWS

How Basepair Differs

No More Data Movement

No need to upload your data to a hosted solution unless you want to. Instead, plug in your own AWS account to leverage both the compute and storage resources that you have already invested in.

Easy to Use for Everyone

Usability how it should be. Point & click interface for the bench scientist, CLI and APIs for the bioinformatician.

Interactive Visualization

Don’t be satisfied with flat files and static HTML pages. Instead, hone in on how you want to see your data through visualizations that dynamically update as you change parameters.

Customized Web Portals

Deploy workflows to end users via white labeled web portals in a matter of weeks. Create unique coupon codes to seamlessly bundle the right amount of analysis at the point of sale of a kit, assay or diagnostic test.

Cost Effective for Every Project

Flexible pricing models ranging from pay-as you-go per sample for smaller projects, to unlimited annual licenses for large scale initiatives. Discounts available for orders placed through AWS marketplace.
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Eliminating data movement translates to enhanced security, zero data duplication and reduced IT costs. Leveraging existing investments in workflows and IT infrastructure reduces technical lock-in.

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Democratizing next generation sequencing (NGS) data analysis reduces data analysis bottlenecks and improves collaboration between the wet and the dry lab. Bioinformatics can spend more time solving difficult problems than on routine analyses.

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Accelerate time to scientific and diagnostic insight so you can speed up R&D projects and reduce turnaround times.

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Business intelligence for your core products that improves customer support. Keep customers in your own brand and ecosystem.

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For commercial software to be a worthwhile investment the license model has to scale cost effectively. Put the savings back into sequencing more samples!

Streamlined Data Import

Seamlessly import data from BaseSpace, NCBI GEO/SRA, and FTP/SFTP with our fully integrated platform.

Custom Workflow Solutions

Our platform enables you to deploy your own custom workflows tailored to your specific needs.

Integrated MultiOmics Solutions

Utilize our interactive platform for comprehensive AWS healthomics analysis, enhancing data insights and research outcomes.

Advanced Data Storage Management

Save up to 80% on your monthly storage bill with fine-grain control over data archival and dynamic retrieval, outperforming S3 intelligent tiering.

Security: Your Data is Safe

Our platform adheres to industry standards, ensuring robust security for your data. Our web interface and API exclusively use HTTPS, encrypting all communication between your device and our servers.

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Ability to seamlessly import data from diverse sources such as BaseSpace, NCBI GEO/SRA, and FTP/SFTP without ever having to leave the Basepair platform. These direct integrations ensures efficient data transfer, simplifying data movement and saving time.

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Empowers users to create efficient, personalized processes that align with their unique requirements. Whether it’s automating data analysis, streamlining tasks, or optimizing resource utilization, these custom workflows enhance productivity and adaptability.

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Integration of AWS HealthOmics lies in the seamless combination of powerful capabilities with an intuitive, user-friendly interface. By having HealthOmics under the hood, users can access advanced features without the complexity typically associated with such tools. This means they can immediately benefit from HealthOmics without investing significant effort in implementation or training.

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Our system automatically moves large Omics files like FASTQ and BAM to cold storage once analysis is complete, eliminating manual management and long delays. When you need to re-analyze samples, the software seamlessly un-archives and initiates the process, ensuring continuous use and substantial cost savings.

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We understand your data is highly valuable. You have complete control over who has access to your data; it can only be accessed by you or other users on Basepair you have explicitly permitted to view or edit your data.

Out-of-the-Box, Industry Standard, Automated Pipelines for Most NGS Data Types. Alternatively, Run Your Own.


  • Whole Genome
  • Whole Exome
  • Targeted Panels
  • Hi-C


  • RNA-Seq
  • Single Cell RNA-Seq


  • ATAC-Seq
  • ChIP-Seq

Home Brew

  • Nextflow
  • WDL
  • YAML
  • Docker
  • GitHub
  • ECR

Learn how automated workflows simplify NGS analysis.

Basepair Work is in Dozens of Peer-Reviewed Journals

"Fast, excellent and reasonably CAN get all three!! Thank you to the folks at Basepair for helping us deal with some difficult RNA Seq data."

Sharen Mckay

Yale University

"I really like how easy the website is to use. And how quickly the results are generated, including figures. I would have never thought about doing a new analysis like I just did."

Emilie Montenont

NYU Langone Health

"Support answers come fast and are always precise!"


Maria Hollnagel

Ulm University

Analyze your NGS data today.

Get results in hours.

You really can do it yourself.