AWS HealthOmics helps life sciences and biotech teams store, query, and analyze genomic, transcriptomic, and other omics data at scale. This workshop recording explains how research, bioinformatics, and cloud teams can use AWS HealthOmics to run reproducible workflows, manage scientific data, and support secure cloud-based analysis on AWS.
Catch highlights from the AWS HealthOmics End-to-End Workshop hosted by Gary Derheim of PTP, featuring Aaron Jeskey from PTP and Ariella Sasson, Amazon HealthOmics Principal Solutions Architect, along with AWS architects Itzik Paz and Sumit Deshpande.
Who Should Watch This AWS HealthOmics Workshop?
This workshop is designed for bioinformaticians, computational biologists, research IT leaders, cloud architects, DevOps teams, and biotech organizations evaluating how to modernize omics data analysis on AWS.
What is AWS HealthOmics?
AWS HealthOmics is a purpose-built service designed for the healthcare and life sciences industry, offering a scalable platform to store, query, and analyze genomic and other biological data. Initially launched as Amazon Omics at re:Invent 2022, the service was renamed at the New York Summit in July 2023.
Addressing Common Challenges in Genomics
Researchers often face challenges managing the size, complexity, and security of genomic data. AWS HealthOmics provides a suite of tools that simplify data storage, analysis, and governance for genomics workflows.
Benefits of AWS HealthOmics
- Multi-omics and Multimodal Analysis: Enables researchers to integrate genomic data with other biological data types.
- Purpose-built Data Storage: Optimized for petabyte-scale storage with cost-effective access and archiving.
- Scalability and Automation: Auto-scale compute resources and automate workflow implementation.
- Enhanced Security and Compliance: Built-in support for HIPAA and GDPR.
Core Components of HealthOmics
- Omics Storage: Secure, compliant storage for FASTQ, BAM, and CRAM files with automatic archiving.
- Bioinformatics Workflows: Use languages like Nextflow, CWL, and WDL to run analyses at scale.
- Variant and Annotation Data: Store and query variant and annotation data using Amazon Athena.
Ready-to-Run Workflows and Analytics
HealthOmics offers pre-configured, ready-to-run workflows priced per execution. These can also be customized to meet specific research needs. Genomic data can be transformed for queryable analytics, enabling multi-modal analysis and collaboration.
Applications and Use Cases
- Population Sequencing: Study genomic variation and connect it to phenotypes.
- Clinical Genomics: Support precision medicine with reproducible workflows.
- Accelerated Clinical Trials: Identify biomarkers and reduce timelines.
- Enhanced Research and Innovation: Improve access to secure genomic data for scientific breakthroughs.
AWS HealthOmics Workshop Transcript Highlights
This chapter guide summarizes the key topics covered in the AWS HealthOmics end-to-end workshop recording, including HealthOmics Storage, Workflows, Analytics, variant annotation, use cases, and related AWS services for life sciences organizations.
Introduction and Overview
0:00 to 1:00
Ariella Sasson introduces AWS HealthOmics, originally launched as Amazon Omics and later renamed in July 2023. This section explains the motivation behind the service and the customer need for more efficient ways to manage genomic, biological, and omics data at scale.
HealthOmics Storage
1:01 to 6:30
AWS HealthOmics Storage provides managed storage for bioinformatics file types such as FASTQ, BAM, and CRAM. It is designed to help life sciences teams store petabytes of omics data efficiently while supporting accessibility, provenance, and lineage.
- Stores data as immutable objects with unique identifiers.
- Supports strict data provenance and lineage.
- Includes archive storage for data that has not been accessed recently.
- Allows archived data to be reactivated through an API call.
HealthOmics Workflows
6:31 to 18:00
AWS HealthOmics Workflows helps teams run bioinformatics analyses at scale using workflow languages such as WDL, Nextflow, and CWL. The workshop explains how containerized tools, private registries, and ready-to-run workflows can support reproducible research pipelines.
- Supports WDL, Nextflow, and CWL workflows.
- Uses OCI-compliant containerized tools stored in Amazon ECR.
- Provides greater visibility into workflow costs and resource usage.
- Includes ready-to-run workflows for analyses such as whole genome and whole exome sequencing.
Analytics and Variant Annotation
18:01 to 28:00
This section explains how AWS HealthOmics transforms genomic data from formats such as GVCF and VCF into Apache Parquet, making the data easier to query and analyze. It also covers how variant and annotation data can be managed separately and queried through AWS analytics services.
- Transforms genomic data into query-ready formats such as Parquet.
- Supports querying through services such as Amazon Athena.
- Decouples variant and annotation data so each can be updated independently.
- Supports fine-grained access controls through AWS Lake Formation.
Use Cases and Benefits
28:01 to 37:00
The workshop highlights HealthOmics use cases such as population sequencing, clinical genomics workflows, clinical trial acceleration, and research innovation. It also explains how life sciences organizations can combine genomic data with clinical context to support more personalized approaches to care.
- Supports population sequencing and large-scale genomic analysis.
- Helps streamline clinical genomics and research workflows.
- Can support clinical trial analysis and cohort discovery.
- Helps organizations build scalable cloud infrastructure with less dependency on internal IT resources.
Additional Capabilities and Roadmap
37:01 to end
The final section introduces related AWS services, including AWS HealthLake, AWS HealthImaging, and AWS HealthScribe. It also discusses ongoing HealthOmics feature development, customer feedback, and resources for teams that want to explore or test AWS HealthOmics.
Explore the Power of AWS HealthOmics
From scientific computing IT support to HIPAA-compliant genomic storage, AWS HealthOmics is built for modern research teams. Discover how PTP automates and optimizes bioinformatics pipelines or explore our CloudOps solution on AWS Marketplace.
Frequently Asked Questions
AWS HealthOmics is a purpose-built service that helps life sciences organizations process and analyze genomic, transcriptomic, and other omics data at scale. It enables researchers to run bioinformatics pipelines, automate workflows, and accelerate scientific discovery using secure cloud infrastructure.
The workshop covers the full lifecycle of genomic data—from ingesting raw sequencing data to running analysis pipelines, visualizing results, and managing compliance. It also includes live demos and architectural walkthroughs of HealthOmics features.
The workshop is ideal for bioinformaticians, clinical researchers, IT leaders in biotech, and DevOps professionals supporting life sciences organizations using AWS for data-intensive workloads.
Yes. AWS HealthOmics supports compliance with regulatory standards such as GxP and HIPAA. It offers encryption, access control, and audit capabilities that help biotech and pharmaceutical organizations meet strict data governance requirements.
Unlike traditional EC2-based pipelines, AWS HealthOmics simplifies pipeline orchestration and automates infrastructure provisioning. It integrates storage, compute, and data access controls into one managed service optimized for omics data.
PTP provides end-to-end support for AWS HealthOmics adoption — including architecture, pipeline migration, security configuration, and compliance readiness — tailored for biotech and research teams accelerating data science in the cloud.