Skip to main content

What's the Difference Between Amazon HealthLake and AWS HealthOmics?

Compare Amazon HealthLake and AWS HealthOmics side by side — features, pricing, and ideal use cases to help you choose the right product.

Compare side-by-side

AWS closed AWS HealthOmics variant stores and annotation stores to new customers, effective November 7, 2025. Existing customers can continue to use them. The HealthOmics sequence store and workflows remain available to new customers.

Comparisons
Amazon HealthLake
AWS HealthOmics
Category

Machine Learning, Healthcare

Machine Learning, Genomics
Description

HIPAA-eligible service to store, transform, and analyze health data using FHIR APIs.

Store, query, and analyze genomic, transcriptomic, and other omics data at scale.
Best for
  • Health data aggregation
  • Clinical analytics
  • Population health
  • Drug safety monitoring
  • Genomic analysis
  • Variant calling
  • Multiomics research
  • Precision medicine
Key features
  • FHIR R4 support
  • NLP enrichment
  • Integrated medical NLP
  • HIPAA eligible
  • Data export
  • Sequence Store
  • Variant Store
  • Annotation Store
  • Workflow engine
  • Ready2Run workflows
Pricing model

Pay per data stored + requests + NLP processing

Pay per GB stored + run hours + queries
Free tier

Limited free allowance: HealthLake Advanced FHIR Subscriptions include 100,000 free events per month for each notification channel (Amazon EventBridge or REST-Hook); Data Store charges still apply.

New AWS customers: monthly allowances for the first 2 months include 275 omics.m.xlarge instance hours (or equivalent) and 49,000 GB-hours of private-workflow run storage; sequence-store allowances of 1,500 gigabase-months each in active and archive storage. Excludes AWS GovCloud (US) Regions; unused monthly usage does not roll over. Restrictions apply. Variant and annotation stores are closed to new customers.
Expert take

“HealthLake stores and transforms healthcare data in FHIR format. Built-in NLP extracts medical entities from clinical notes and normalizes them to standard ontologies.”
— Didier Durand, re:Post Top Contributor [profile]

“HealthOmics stores and analyzes genomic data at petabyte scale. Ready-to-run workflows process whole genomes in hours using optimized bioinformatics pipelines.”
— Gary McLean, re:Post Top Contributor [profile]
Product page

Learn more about Amazon HealthLake »

Learn more about AWS HealthOmics »

When to use Amazon HealthLake or AWS HealthOmics

Use Amazon HealthLake when:

  • Health data aggregation
  • Clinical analytics
  • Population health
  • Drug safety monitoring

Learn more about Amazon HealthLake »

Use AWS HealthOmics when:

  • Genomic analysis
  • Variant calling
  • Multiomics research
  • Precision medicine

Learn more about AWS HealthOmics »

AWS product comparisons

Read about AWS products side-by-side

Displaying 1-8 (21)
2026-07-30

What's the difference between Amazon Aurora and Amazon Neptune?

Both are purpose-built, fully managed AWS databases, but they solve fundamentally different problems. Aurora handles structured relational data with SQL; Neptune handles highly connected data where relationships between entities are the primary query pattern.
Learn more
2026-07-30

What's the difference between Amazon RDS and Amazon Redshift?

Both run SQL queries, but they're optimized for fundamentally different workloads. RDS handles transactional operations (inserts, updates, lookups) for your application. Redshift handles analytical queries (aggregations, scans, joins across billions of rows) for your data team.
Learn more
2026-07-30

What's the difference between Amazon Aurora and Amazon DynamoDB?

Both are fully managed AWS database services, but they serve fundamentally different data models and access patterns. Aurora is a relational database for structured data with relationships; DynamoDB is a NoSQL key-value store built for single-digit millisecond performance at any scale.
Learn more
2026-07-30

What's the difference between Amazon DocumentDB and Amazon Neptune?

Both handle semi-structured data, but they're optimized for different query patterns. DocumentDB stores and queries JSON documents; Neptune stores and traverses relationships between entities.
Learn more
2026-07-30

What are the differences between Amazon DynamoDB and Amazon DocumentDB?

Both are fully managed NoSQL databases on AWS, but they serve different data models. DynamoDB is a key-value store optimized for known access patterns at massive scale; DocumentDB is a document database for flexible JSON schemas with MongoDB compatibility.
Learn more
2026-07-30

What's the difference between Amazon DynamoDB and Amazon Keyspaces?

Both are fully managed, serverless-capable NoSQL databases on AWS. DynamoDB is AWS-native with its own API and data model; Keyspaces is Apache Cassandra-compatible, letting you use existing Cassandra drivers, tools, and expertise.
Learn more
2026-07-30

What's the difference between Amazon ElastiCache and Amazon MemoryDB?

Both are Redis-compatible, fully managed in-memory services on AWS. ElastiCache is designed as a caching layer in front of another database; MemoryDB is designed as a primary database that combines in-memory speed with Multi-AZ durability.
Learn more
2026-07-30

What's the difference between Amazon Aurora and Amazon RDS?

Both are fully managed relational database services on AWS, but Aurora is a cloud-native engine built for higher performance and availability, while RDS gives you familiar open-source and commercial engines with less operational overhead than self-managed.
Learn more

Did you find what you were looking for today?

Let us know so we can improve the quality of the content on our pages