MCP Server

Overview

Endpoint: https://subseq.bio/mcp (HTTP transport, JSON-RPC 2.0 over POST).

Once configured, agents can use the same public API surface as the web UI for jobs, datasets, projects, and account info. Agents will be instructed to use pre-signed URLs instead of auth file downloads.

Note: This allows agents to autonomously delete data and use your account credits. The MCP server is experimental with ongoing improvements. Use carefully.

Authentication

Auth is bearer token only: send Authorization: Bearer <api_key>. OAuth is not supported yet (ChatGPT and claude.ai require OAuth).

1. Click your email (top-right) in the UI.
2. Open API Keys.
3. Click New Key.
4. Save it locally as SUBSEQ_API_KEY.

Client Config Examples

Claude Code

export SUBSEQ_API_KEY=<your_subseq_api_key>
claude mcp add --transport http subseq https://subseq.bio/mcp --header "Authorization: Bearer ${SUBSEQ_API_KEY}"

Codex

export SUBSEQ_API_KEY=<your_subseq_api_key>
codex mcp add subseq --url https://subseq.bio/mcp --bearer-token-env-var SUBSEQ_API_KEY

Cursor

Command Palette -> "MCP" -> Open MCP Settings -> New MCP Server. Use the following mcp.json:

{
  "mcpServers": {
    "subseq": {
      "url": "https://subseq.bio/mcp",
      "headers": {
        "Authorization": "Bearer <your_subseq_api_key>"
      }
    }
  }
}

Tools, Resources, and Downloads

Tools mirror the public REST API (jobs, datasets, projects, account info, pricing, status). Use tools/list for the full set.

For usage help, call tool_usage or program_usage, or browse resources under subseq://usage/tools/<tool> and subseq://usage/programs/<program>.

File uploads via MCP are intended for small inputs only (the file bytes must be included directly in the tool call). MCP upload limits: up to 256 files, up to 2 MiB total, up to 512 KiB per file. For large folders/files, use the web UI or a CLI workflow.

Protocol Compatibility

The server implements MCP HTTP transport with one JSON-RPC 2.0 request per POST. The MCP-Protocol-Version header is optional; the server replies with the negotiated version.

Server identifier: subseq-mcp v0.2.0. tools/resources listChanged notifications are not emitted.