Basespace Illumina Illumina BaseSpace API
✓ Official Vendor SpecHealthcareClinical Databearer,apiKey29 EndpointsREST
For Agents
Browse and manage Illumina sequencing runs, projects, samples, and files in BaseSpace Sequence Hub. Useful for agents automating bioinformatics pipelines or sample tracking.
Use for: I need to list all sequencing runs for the current user, Retrieve the FASTQ files for sample 12345, Create a new BaseSpace project for the cohort study, List app results in project ABC
Not supported: Does not handle variant calling, alignment, or sequencing instrument control — use for browsing and managing runs, projects, samples, and files in BaseSpace Sequence Hub only.
BaseSpace Sequence Hub is Illumina's cloud platform for genomic sequencing data, and the BaseSpace API exposes programmatic access to runs, projects, samples, files, and app results. It supports authenticated lookup of the current user, listing and management of sequencing projects, retrieval of FASTQ and BAM file content, and OAuth 2.0 token issuance for app integrations. The API is the standard integration point for bioinformatics pipelines, LIMS systems, and analysis tooling that need to read or write data alongside an Illumina sequencer.
Install Jentic One Beta
Connect the Illumina BaseSpace API to your agent
Jentic One is a self-hosted execution layer for AI agents. It lets your agent call the Illumina BaseSpace 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://raw.githubusercontent.com/jentic/jentic-one/main/tools/install.sh | sh2
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 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 BaseSpace API.
Look up the authenticated user and list their associated sequencing runs
Create and manage projects that group sequencing samples and analyses
Retrieve sample metadata and download FASTQ or BAM file content
List app results produced by BaseSpace analysis apps for a given project
Issue OAuth 2.0 access tokens for app integrations using POST /oauthv2/token
Delete obsolete runs, samples, or app results to manage storage
Use Cases
Patterns agents use Illumina BaseSpace API for, with concrete tasks.
★ Bioinformatics Pipeline Ingestion
An automated pipeline needs to pick up newly completed sequencing runs and pull the resulting FASTQ files into a downstream analysis system. The BaseSpace API exposes GET /users/current/runs for run discovery, GET /runs/{id}/files to enumerate outputs, and GET /files/{id}/content to stream the data. Projects with hundreds of samples can be processed by paging through the listing endpoints.
Call GET /users/current/runs, find the most recent completed run, list its files via GET /runs/{id}/files, and stream each file with GET /files/{id}/content
Sample and Project Management
Lab managers organising sequencing output by study or cohort can use the API to create projects, attach samples, and tear down completed work. Endpoints include POST /projects to create a project, GET /projects/{id}/samples to list its samples, and DELETE /samples/{id} or DELETE /projects/{id} to clean up. The flow integrates with LIMS systems that treat BaseSpace as the storage tier for sequencing output.
Call POST /projects to create a project named cohort-A, then list samples with GET /projects/{id}/samples and delete any flagged with QC failures via DELETE /samples/{id}
App Result Retrieval
BaseSpace apps run analyses (alignment, variant calling, QC) and write results back into projects as app results. Downstream systems can list these via GET /projects/{id}/appresults and fetch specific outputs with GET /appresults/{id}, allowing automated reporting tools to surface variant calls or QC summaries without manual export from the BaseSpace UI.
Call GET /projects/{id}/appresults for a project, fetch each app result with GET /appresults/{id}, and post a summary into the lab notebook
Agent-Driven Sample Lookup via Jentic
An AI agent embedded in a lab assistant tool can use BaseSpace through Jentic to answer scientist questions like 'show me the latest run for sample X' without the operator hand-rolling auth. Jentic isolates the OAuth 2.0 access token in its vault and exposes the 29 BaseSpace operations as discoverable tools, mapped to natural-language search queries.
Search Jentic for 'list sequencing runs for current user', load the GET /users/current/runs schema, and execute to return the latest run summary
Key Endpoints
29 endpoints — basespace sequence hub is illumina's cloud platform for genomic sequencing data, and the basespace api exposes programmatic access to runs, projects, samples, files, and app results.
METHOD
PATH
DESCRIPTION
GET
/users/current/runs
List sequencing runs for the authenticated user
GET
/runs/{id}
Fetch metadata for a specific run
POST
/projects
Create a new BaseSpace project
GET
/projects/{id}/samples
List samples within a project
GET
/files/{id}/content
Stream the binary content of a file
GET
/projects/{id}/appresults
List analysis app results in a project
POST
/oauthv2/token
Issue an OAuth 2.0 access token
GET
/users/current/runs
List sequencing runs for the authenticated user
GET
/runs/{id}
Fetch metadata for a specific run
POST
/projects
Create a new BaseSpace project
GET
/projects/{id}/samples
List samples within a project
GET
/files/{id}/content
Stream the binary content of a file
GET
/projects/{id}/appresults
List analysis app results in a project
POST
/oauthv2/token
Issue an OAuth 2.0 access token
Why Jentic?
Three things that make agents converge on Jentic-routed access.
Credential isolation
BaseSpace OAuth 2.0 access tokens are stored encrypted in the Jentic vault. Agents receive scoped credentials, so the raw bearer token never sits in the agent's prompt or memory when calling endpoints like GET /files/{id}/content.
Intent-based discovery
Agents search by intent (e.g. 'list sequencing runs' or 'download FASTQ files') and Jentic returns matching BaseSpace operations with their input schemas and parameter requirements.
Time to first call
Direct BaseSpace integration: 1-3 days for OAuth setup, error handling, and file streaming. Through Jentic: under an hour — search, load schema, execute.
Related APIs
Alternatives and complements available in the Jentic catalogue.
FAQs
Specific to using Illumina BaseSpace API through Jentic.
What authentication does the Illumina BaseSpace API use?
BaseSpace uses OAuth 2.0 bearer tokens, with an additional access token header scheme available. Issue a token via POST /oauthv2/token, then pass it as Authorization: Bearer <token>. Through Jentic the token is stored encrypted in the vault and never enters the agent's context.
Can I download FASTQ files with the Illumina BaseSpace API?
Yes. List a sample's files via GET /samples/{id}/files, then stream each file with GET /files/{id}/content. Files are returned as their native binary format (FASTQ, BAM, etc.) — for large files, use range requests or streaming clients.
How do I list a user's sequencing runs through Jentic?
Search Jentic for 'list sequencing runs for current user', which surfaces GET /users/current/runs. Load the schema and execute. Jentic returns a paginated list of runs the authenticated BaseSpace user owns or has access to.
What are the rate limits for the BaseSpace API?
The OpenAPI spec does not declare explicit rate limits. Illumina applies per-account quotas and may throttle large file downloads — check the BaseSpace developer portal for current limits before running batch ingestion.
Can I create a new project with the BaseSpace API?
Yes. Call POST /projects with the project name and description. The response returns the new project ID, which you can pass to GET /projects/{id}/samples or POST /projects/{id}/appresults to attach related resources.
Does the BaseSpace API support deleting old runs and samples?
Yes. The API exposes DELETE /runs/{id}, DELETE /samples/{id}, DELETE /projects/{id}, and DELETE /appresults/{id}. Use these carefully — deletion is generally irreversible and will free associated file storage.
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