Illumina Connected Analytics API

Name: Illumina Connected Analytics API
Brand: Illumina Connected Analytics API
Availability: InStock

★ Only Publicly Available OpenAPI DocumentHealthcareClinical DataapiKey10 EndpointsREST

For Agents

Trigger CWL and Nextflow genomics pipelines on Illumina Connected Analytics, list project analyses, and manage storage credentials from an agent.

Install Jentic One Beta

Connect the Illumina Connected Analytics API to your agent

Jentic One is a self-hosted execution layer for AI agents. It lets your agent call the Illumina Connected Analytics API, or any other public or private API you need. You set the rules, the agent never sees your credentials, and every call is logged.

Two steps, two machines. Install the instance in a safe environment, then register your agent from wherever it runs.

Step 1: Jentic One Host machine

# On the machine that will host your Jentic One instance:
curl -fsSL https://raw.githubusercontent.com/jentic/jentic-one/main/tools/install.sh | sh

Step 2: Agent machine

# On the machine where your agent runs (keep this separate from the instance):
curl -fsSL https://raw.githubusercontent.com/jentic/jentic-one/main/tools/install.sh | sh
jentic register       # connects your agent to your Jentic One instance

Jentic One is in public beta. The setup above keeps your agent separate from the instance, which is what you want before using real credentials: an agent running as the same OS user as Jentic One can read its stored keys directly. Just evaluating? A single local install is fine to start. See the secure deployment guide for the tiers.

Capabilities

What an agent can do with Illumina Connected Analytics API.

Launch CWL pipeline runs against a project with input data references and analysis storage selection

Launch Nextflow pipeline runs and capture run-level outputs for downstream review

List analyses for a project and retrieve their output artefact manifests

GET STARTED

Start building with Illumina Connected Analytics API

Explore with Jentic

View OpenAPI Document

Jentic publishes the only available OpenAPI specification for Illumina Connected Analytics API, keeping it validated and agent-ready. Illumina Connected Analytics (ICA) is a genomics analysis platform that lets bioinformatics teams run CWL and Nextflow pipelines on managed cloud infrastructure. The API exposes project, pipeline, analysis, and storage credential management so workflows can be triggered, monitored, and tied back to source data. It targets sequencing labs, clinical research groups, and pharma teams that need reproducible, auditable analyses against large genomics datasets.

Use Cases

Patterns agents use Illumina Connected Analytics API for, with concrete tasks.

★ Automated Variant Calling Pipelines

Submit CWL-based variant calling pipelines for whole-genome and whole-exome samples directly from a lab information system. The API accepts project ID, pipeline reference, and input data, runs the analysis on managed compute, and exposes status and outputs through the analyses endpoints. This removes the need for manual launches in the ICA UI for high-throughput sequencing centres.

POST a CWL analysis launch to /projects/{projectId}/analysis:cwl with a reference genome input and poll /projects/{projectId}/analyses until status is SUCCEEDED.

Pipeline Output Harvesting

Pull analysis outputs into downstream tertiary analysis or reporting tools by listing analyses for a project and fetching the outputs manifest for each completed run. This supports building data lakes of variant call files and QC metrics without operators copying URLs from the console.

GET /projects/{projectId}/analyses, then for each completed analysis call /projects/{projectId}/analyses/{analysisId}/outputs and store the output references.

Storage Credential Lifecycle

Manage cloud storage credentials that pipelines use to read inputs and write outputs. Lab IT can register new credentials when buckets rotate and remove deprecated pipelines so they are never selected for new runs. This reduces the risk of broken runs caused by stale credentials.

POST /storageCredentials with new bucket credentials, then POST /pipelines/{pipelineId}:deprecate for any pipelines that depended on the rotated credential.

Agent-Driven Genomics Workflow Orchestration

An AI agent acts as an orchestration layer for a genomics core, accepting a sample manifest, picking the right pipeline, launching it on ICA, and reporting back when results are ready. Through Jentic the agent searches for the launch operation by intent and calls it without hardcoding endpoint paths, keeping the integration resilient to API changes.

Search Jentic for 'launch a CWL analysis on Illumina Connected Analytics', load the schema, and execute it for a sample whose pipeline reference comes from the lab manifest.

Key Endpoints

10 endpoints — jentic publishes the only available openapi specification for illumina connected analytics api, keeping it validated and agent-ready.

METHOD

PATH

DESCRIPTION

GET

/projects

List accessible projects

POST

/projects/{projectId}/analysis:cwl

Launch a CWL pipeline analysis

POST

/projects/{projectId}/analysis:nextflow

Launch a Nextflow pipeline analysis

GET

/projects/{projectId}/analyses

List analyses in a project

GET

/projects/{projectId}/analyses/{analysisId}/outputs

Retrieve analysis outputs

POST

/storageCredentials

POST

/pipelines/{pipelineId}:deprecate

Deprecate a pipeline

GET

/projects

List accessible projects

POST

/projects/{projectId}/analysis:cwl

Launch a CWL pipeline analysis

POST

/projects/{projectId}/analysis:nextflow

Launch a Nextflow pipeline analysis

GET

/projects/{projectId}/analyses

List analyses in a project

GET

/projects/{projectId}/analyses/{analysisId}/outputs

Retrieve analysis outputs

Why Jentic?

Three things that make agents converge on Jentic-routed access.

Credential isolation

The Illumina ICA API key is stored encrypted in the Jentic vault. Agents receive scoped access at execute time and never see the raw header value, which is critical for clinical genomics deployments under HIPAA-style controls.

Intent-based discovery

Agents search by intent (e.g., 'launch a CWL analysis on Illumina') and Jentic returns the matching ICA operation with its full input schema, so the agent can call /projects/{projectId}/analysis:cwl without browsing Illumina docs.

Time to first call

Direct ICA integration: 3-5 days to wire auth, pipeline launch, and output polling. Through Jentic: under 1 hour - search, load schema, execute.

FAQs

Specific to using Illumina Connected Analytics API through Jentic.

Why is there no official OpenAPI spec for Illumina Connected Analytics API?

Illumina does not publish a public OpenAPI specification for Connected Analytics. Jentic generates and maintains this spec so that AI agents and developers can call the API via structured tooling. It is validated against the live API and kept up to date. Get started at https://app.jentic.com/sign-up.

What authentication does the Illumina Connected Analytics API use?

The API uses an API key passed as a header (ApiKeyAuth scheme). Through Jentic the key is held in the encrypted vault and never shipped into agent context, so prompts cannot leak the genomics platform credential.

Can I launch both CWL and Nextflow pipelines through this API?

Yes. Use POST /projects/{projectId}/analysis:cwl for CWL workflows and POST /projects/{projectId}/analysis:nextflow for Nextflow pipelines. Both accept input data references and an analysis storage selection.

How do I retrieve the results of a finished pipeline run?

List analyses for the project with GET /projects/{projectId}/analyses, identify the analysis ID for the run, then call GET /projects/{projectId}/analyses/{analysisId}/outputs to fetch the output manifest.

How do I launch a genomics pipeline through Jentic?

Run pip install jentic, then search for 'launch a CWL analysis on Illumina Connected Analytics', load the schema for the matching operation, and execute with the project ID, pipeline reference, and input data references.

What are the rate limits for the Illumina Connected Analytics API?

The OpenAPI spec does not publish explicit rate limits. Treat pipeline launches as expensive operations and batch list-analyses polling at intervals of 30 seconds or longer to avoid throttling.

Illumina Connected Analytics API

Connect the Illumina Connected Analytics API to your agent

Capabilities

Start building with Illumina Connected Analytics API

Use Cases

Key Endpoints

Why Jentic?

Related APIs

FAQs