Bioinformatics on AWS, made even
Easier Faster More Cost Predictable
Basepair is the first and only Software-as-a-Service (SaaS) platform that provisions in your own AWS account to deliver out-of-the-box direct integration with AWS HeathOmics, putting you in control of your IT governance, compliance and usage commitments on AWS.

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

Trusted by Industry Leaders at


Simplyfying Bioinformatics on AWS

Traditional commercial tools fall short by requiring data movement into a hosted solution for either compute, storage or both. It’s time for a new approach to bioinformatics.

Using internal bioinformatics and IT headcount to set up a secure, scalable infrastructure on AWS can be involved, resource intensive and time consuming


What if there was a platform that delivered the ultra-low operational burden of SaaS, together with the control of leveraging the compute & storage resources, to automate the migration, deployment and orchestration of AWS HealthOmics workflows at scale?

Analyzing and making sense of next generation sequencing (NGS) data is often left entirely to the purview of bioinformatics, creating an unnecessary bottleneck.


What if there was a way to easily deploy ready to run or private AWS HealthOmics workflows via a point & click graphical user interface so that more scientists could analyze and interactively explore NGS data before collaborating with bioinformatics on an informed question?

Developing complete software applications in house requires a dedicated team of specialist individuals and takes months if not years to get to market.


What if you could in-license your own branded software application to make available to your customers without having to hire or repurpose resources, all whilst retaining the ability to bundle analysis at the point of sale of your core product or service?

Democratize Omics Data Analysis with Basepair on AWS HealthOmics



Point & Click Graphical User Interface


Built in enterprise platform capabilities such as Login/Access Controls, Import/Export of data, Performance & Certifications / Compliance

Cost Predictable

AWS HealthOmics can be up to 50% cheaper than S3 intelligent tiering


Out of the box interactive visualization for rapidly understanding the meaning and value of your data.

Bioinformatics on AWS

Leverage the storage and compute resources in your own AWS account

Amount of time needed to learn the platform

< 10 minutes

Accelerate time to production by 

up to 8X

Reduce compute & storage costs by up to



Time saved in routine analysis of raw data


Reduce Data compliance and IT Governance overhead by up to



AWS Ready To Run Workflows
  • GATK-BP Germline fq2vcf for 30x genome
  • NVIDIA Parabricks Germline HaplotypeCaller WGS for up to 5X
  • AlphaFold for 601-1200 residues
  • ScRNAseq with KallistoBUStools
  • NVIDIA Parabricks FQ2BAM WGS for up to 30X
  • AlphaFold for up to 600 residues
  • Bases2Fasta for 2×75
  • GATK-BP fa2bam
  • NVIDIA Parabricks Germline HaplotypeCaller WGS for up to 30X
  • NVIDIA Parabricks FQ2BAM WGS for up to 5X
  • Bases2Fasta for 2×150
  • NVIDIA Parabricks Germline DeepVariant WGS for up to
  • ESMFold for up to 800 residues
  • Ultima Genomics DeepVariant for up to 40
AWS HealthOmics Sequence Store
  • Automated Data Movement Through S3 into and Out of Sequence Store
  • Archived Omics ReadSets are automatically activated upon utilization in workflow execution
  • Connected Cloud capability enables customers to integrate their own cloud infrastructure for sample storage
Basepair Native Supported Application Areas
  • Genomics (WGS, WES, Panels, CRISPR etc)
  • Transcriptomics (bulk and single cell RNASeq)
  • Epigenetics (ATACSeq, ChIPSeq, CUT&RUN, CUT&TAG etc)
  • Metagenomics (16S, Shotgun etc)

“Using Basepair to deploy routine analyses to our bench scientists has freed up about 25% of our time to focus on more valuable data mining tasks. What’s more, bench scientists now come to my team with an informed question rather than a request to work on small, repetitive tasks, improving collaboration between R&D teams.”

Sombeet Sahu

Associate Director, Bioinformatics, Nkarta Therapeutics

Connect With Our Team Today To Learn More!