What is AWS HealthOmics?
AWS HealthOmics is a HIPAA-eligible service that takes on the complex infrastructure behind bioinformatics analysis. AWS describes it as fully managed bioinformatics workflows for clinical diagnostic testing, drug discovery and agricultural research.
You bring your existing pipelines in the industry-standard workflow languages WDL, Nextflow and CWL; AWS provides the compute capacity and scales it automatically. AWS states that workflows scale across 100,000+ concurrent vCPUs to support tens of thousands of tests daily.
Core capabilities
- Managed workflows: Execution of pipelines in WDL, Nextflow and CWL without operating your own cluster
- Automatic scaling: Compute capacity provided by AWS, stated at more than 100,000 concurrent vCPUs
- Omics data stores: Sequence store for sequence data with active and archive tiers
- Compliance capabilities: HIPAA eligibility, built-in audit trails and data provenance tracking
- Ready2Run workflows: Prebuilt workflows charged at a flat fee per successful run
- Cost per sample: A predictable cost structure per sample instead of upfront infrastructure investment
Typical use cases
Clinical diagnostics: Laboratories run sequencing pipelines with the traceable data provenance and audit trail that clinical processes require.
Drug discovery: Research teams process large omics data sets without operating dedicated HPC clusters.
Agricultural research: Genomic analysis in plant and animal breeding uses the same managed workflows.
Benefits
- Existing pipelines in WDL, Nextflow and CWL remain usable
- No HPC infrastructure to operate yourself
- Built-in compliance and traceability capabilities
- Usage-based billing with a predictable cost per sample
Note on scope
Per the AWS service availability announcement of 13 October 2025, the Variant and Annotation Store capability has not been accessible to new customers since 7 November 2025 and is in maintenance mode. Check before designing whether your architecture depends on that store type.
Integration with innFactory
As an AWS Reseller, innFactory supports you with AWS HealthOmics: migrating existing Nextflow or WDL pipelines, setting up sequence stores, modelling cost per sample, and aligning data protection and compliance requirements for health data in EU Regions.
Typical Use Cases
Technical Specifications
Frequently Asked Questions
What is AWS HealthOmics?
AWS HealthOmics is a HIPAA-eligible service for fully managed bioinformatics workflows. It manages the complex infrastructure behind clinical diagnostic testing, drug discovery and agricultural research.
Which workflow languages are supported?
AWS HealthOmics supports the industry-standard workflow languages WDL, Nextflow and CWL. Existing pipelines can therefore be reused while AWS provisions and scales the underlying infrastructure automatically.
How does the service scale?
AWS states that workflows scale across 100,000+ concurrent vCPUs to support tens of thousands of tests daily. Scaling happens automatically, without you operating clusters yourself.
How is AWS HealthOmics billed?
Billing is usage-based. For private workflows you pay for the omics instance used by each task plus run storage, billed in increments of one second with a minimum of 60 seconds per task. Ready2Run workflows are charged a flat fee when runs complete successfully. Sequence stores are charged per gigabase per month.
Are any parts of the service being retired?
Yes. Per the AWS service availability announcement of 13 October 2025, the Variant and Annotation Store capability has not been accessible to new customers since 7 November 2025 and is in maintenance mode. The workflow capabilities and the sequence store are not affected.
Note: All product information on this page has been compiled with care, but is provided without guarantee and may be outdated or incomplete. Cloud services evolve rapidly — features, pricing, SLAs, and availability change frequently. Authoritative and up-to-date information can only be found on the official product page of AWS (official documentation). This page does not represent an offer by AWS.