Illumina Connected Analytics API
Official vendor OpenAPI document · agent-readyHealthcareClinical DataapiKey10 EndpointsREST
For Agents
Lets an AI agent launch CWL and Nextflow genomics pipelines on Illumina Connected Analytics, track analyses within a project, and download their outputs.
Use for: I need to run a genomics pipeline on a sequencing dataset, Start a Nextflow analysis in a specific project, Download the outputs of a completed analysis, List the analyses that have run in a project
Not supported: Does not handle sequencing instrument control, variant interpretation, or clinical reporting. Use it for launching and retrieving genomics pipeline analyses only.
Illumina Connected Analytics is a genomics analysis platform API for running bioinformatics pipelines in the cloud. It starts CWL and Nextflow pipeline executions within a project, lists analyses and fetches their outputs, and reports the available analysis storage options. Projects, pipelines, and external storage credentials are managed through the same interface, giving genomics teams programmatic control over large-scale sequencing analysis.
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.
1
Step 1: Jentic One Host machine
# On the machine that will host your Jentic One instance:
curl -fsSL "https://jentic.com/install.sh?src=apis&api=%2Fapis%2Fillumina.com%2Filluminaconnectedanaly" | sh2
Step 2: Agent machine
# On the machine where your agent runs (keep this separate from the instance):
curl -fsSL "https://jentic.com/install.sh?src=apis&api=%2Fapis%2Fillumina.com%2Filluminaconnectedanaly" | sh
jentic register # connects your agent to your Jentic One instanceJentic 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.
List genomics projects and their available storage options
Start CWL pipeline executions within a project
Start Nextflow pipeline executions within a project
Retrieve analyses and download their outputs
Register external storage credentials for analysis data
Manage pipeline lifecycle including archive and deprecation
Use Cases
Patterns agents use Illumina Connected Analytics API for, with concrete tasks.
★ Cloud genomics pipeline execution
A bioinformatics team needs to run CWL or Nextflow pipelines on sequencing data without managing its own compute. Illumina Connected Analytics launches a pipeline within a project, tracks the resulting analysis, and exposes the outputs for retrieval, so a team can move from a dataset to results through the interface. Storage options are reported per analysis.
Start a Nextflow pipeline execution in a project and record the returned analysis identifier
Analysis output retrieval
Downstream tools need the files a pipeline produced. The API lists the analyses in a project and fetches the outputs for a completed run, letting a workflow collect result files as soon as an analysis finishes. Listing is paginated so large projects can be walked in order.
List completed analyses in a project and fetch the outputs for the most recent one
AI agent genomics workflow
An AI agent coordinating a genomics workflow can launch a pipeline, poll for completion, and gather outputs without manual steps. The agent selects the project, starts the CWL or Nextflow run, and retrieves results, with pipeline launches gated behind operations the lab has allowed. Read-only listing keeps monitoring separate from execution rights.
Given a project and pipeline, start the analysis, wait for completion, and download its outputs
Key Endpoints
10 endpoints — illumina connected analytics is a genomics analysis platform api for running bioinformatics pipelines in the cloud.
METHOD
PATH
DESCRIPTION
GET
/projects
List projects
POST
/projects/{projectId}/analysis:cwl
Start a CWL pipeline execution
POST
/projects/{projectId}/analysis:nextflow
Start a Nextflow pipeline execution
GET
/projects/{projectId}/analyses
List analyses in a project
GET
/projects/{projectId}/analyses/{analysisId}/outputs
Fetch analysis outputs
GET
/analysisStorages
List available analysis storage options
GET
/projects
List projects
POST
/projects/{projectId}/analysis:cwl
Start a CWL pipeline execution
POST
/projects/{projectId}/analysis:nextflow
Start a Nextflow pipeline execution
GET
/projects/{projectId}/analyses
List analyses in a project
GET
/projects/{projectId}/analyses/{analysisId}/outputs
Fetch analysis outputs
GET
/analysisStorages
List available analysis storage options
Why Jentic?
What agents get from Jentic-routed access to this vendor.
Setup
Wiring Illumina Connected Analytics by hand means provisioning an API key, learning the project-scoped analysis paths, and building the CWL and Nextflow launch payloads. Install Jentic One once, import the API from the Jentic API Directory, and store the credential once for your agent to reuse.
Permission scoping
Scope your agent to read-only operations such as listing projects and fetching outputs, and, because the project is a path parameter on the analysis operations, restrict it to a single project. You decide which operations are callable.
Credential isolation
Your Illumina API key is stored once, encrypted, by your own Jentic One instance and injected only at execution time. It never enters the agent's prompt, logs, or context.
Intent-based discovery
Agents find Illumina Connected Analytics through Jentic's intent search: a query such as 'run a genomics pipeline' matches the analysis and project operations, which the agent then calls with your stored credential.
Related APIs
Alternatives and complements available in the Jentic catalogue.
FAQs
Specific to using Illumina Connected Analytics API through Jentic.
What can an AI agent do with the Illumina Connected Analytics API?
An agent can list projects and storage options, start CWL and Nextflow pipeline executions within a project, list analyses, and download the outputs of a completed run. It covers launching and retrieving genomics analyses.
How does the Illumina Connected Analytics API authenticate?
It authenticates with an API key sent in an X-API-Key header on each request. Jentic injects the key at execution time so it stays out of the agent's context.
Can I limit what my agent is allowed to do with the Illumina Connected Analytics API?
Yes. Your Jentic One instance decides which operations an agent may call, so you can allow read-only listing and output retrieval while withholding pipeline launches. Because the project is a path parameter, you can also confine an agent to a single project.
Which pipeline languages does the platform run?
It runs both CWL and Nextflow pipeline executions within a project, and returns the resulting analyses and their outputs for download once a run completes.
How do I connect the Illumina Connected Analytics API to my AI agent with Jentic?
Install Jentic One with its setup script, import the API from the Jentic API Directory, and store your API key once. Your agent can then call the project, analysis, and output operations you allow.
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