AWS HealthOmics resources

User Guide

Learn how to use AWS HealthOmics in this step-by-step developer guide.

API Reference

Read this reference guide for AWS HealthOmics APIs and parameters.

Tutorials

HealthOmics End-to-End Workshop

Get started with HealthOmics workflows and storage

HealthOmics Tutorials

Open source repository on GitHub with example code that demonstrates how to store, process, and query genomic and biological datasets using AWS HealthOmics

Workflow Tools

Drug Discovery Workflows

Use this collection of AWS HealthOmics workflows to accelerate drug discovery

Example Workflows

Build private workflows based on open source HealthOmics workflow examples

Run Analyzer

Run analyzer is a run performance optimization tool that retrieves run manifests logs from CloudWatch and generates statistics for a run, including CPU and memory utilization for each workflow task

WDL Linter

Use the HealthOmics WDL linter to detect common workflow errors before running workflows

Nextflow Linter

Lint for common Nextflow errors before a workflow script is run

ECR Helper

Migrate existing containers to your private ECR repository using the ECR helper tool

Re-run Tool

Re-run archived runs from CloudWatch run manifest logs

Data Storage Tools

Read Set Transfer Manager

Easily download files from a AWS HealthOmics reference or read set

Event Driven Importer

CDK app demonstrating an event-driven architecture that automates importing data into AWS HealthOmics sequence stores when objects are created in Amazon S3.

Sequence Store Manifest Generator

Generates a json manifest for AWS HealthOmics sequence store import jobs

Sequence Store Duplicate Read Set Finder

Identifies duplicate read sets stored in AWS HelathOmics sequence stores

Solutions

Guidance for a Laboratory Data Mesh on AWS

This Guidance demonstrates how to build a scientific data management system that integrates both laboratory instrument data and software systems, such as electronic lab notebooks (ELNs) and lab information management systems (LIMS), with HealthOmics.

Guidance for Digital Connected Lab on AWS

This Guidance helps you to connect life sciences data instruments and laboratory system files to the AWS Cloud, either through the internet or a direct connection with low latency.

Guidance for Migration & Storage of Sequence Data with AWS HealthOmics

This Guidance demonstrates how to import omics sequence data from Amazon Simple Storage Service (Amazon S3) into AWS HealthOmics Storage.

Guidance for Multi-Modal Data Analysis with AWS Health and ML Services

This Guidance demonstrates how to set up an end-to-end framework to analyze multimodal healthcare and life sciences (HCLS) data.

Guidance for Bioinformatics Workflows on AWS

This Guidance shows how you can build and run production-grade bioinformatics workflows at scale and use AWS services for automation, workflow analysis, storage, and operational and cost observability.