Illumina BaseSpace API

Name: Illumina BaseSpace API API
Brand: Illumina BaseSpace API
Availability: InStock

✓ 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.

Quickstart

Get started with Illumina BaseSpace API in minutes using your preferred integration method.

# Add to your MCP client config (Claude Desktop, Cursor, Windsurf)
{
  "jentic": {
    "url": "https://api.jentic.com/mcp",
    "auth": "oauth"
  }
}

# Then ask your agent:
"list illumina sequencing runs"

# → Jentic returns the GET /events tool with parameter schema, agent executes.

Capabilities

What an agent can do with Illumina BaseSpace API 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

GET STARTED

Start building with Illumina BaseSpace API API

Explore with Jentic

View OpenAPI Document

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.

Use Cases

Patterns agents use Illumina BaseSpace API 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

Why though 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.

Complementary

Baseten API

ML model deployment — pair with BaseSpace to serve genomics models on top of sequencing data

Choose Baseten when the task is deploying or invoking an ML model; BaseSpace when fetching the sequencing input data.

Complementary

Basesnap API

Database snapshot service — useful for snapshotting LIMS databases that index BaseSpace samples

Use Basesnap to back up state databases that link to BaseSpace samples; not a direct BaseSpace alternative.

Alternative

BC Laws

Unrelated domain; included because no genomics-API competitor exists in the corpus

Not a real alternative — only listed as a placeholder while the corpus lacks a genomics peer.

FAQs

Specific to using Illumina BaseSpace API 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.