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Version: 26.1

Co-Scientist

Co-Scientist is Seqera's AI assistant for bioinformatics. It builds, runs, and debugs Nextflow pipelines, manages your data, and works with your Seqera Platform resources.

In Seqera Platform Enterprise, Co-Scientist is available on two surfaces:

  • In the Seqera CLI: Run seqera ai in your terminal to work in your local checkout with access to your Platform workspace. See Installation.
  • In the Co-Scientist web interface: The browser interface deployed alongside your installation, including projects.

Both surfaces use the same assistant and the same Seqera Platform Enterprise account.

note

Co-Scientist is not part of a default Seqera Platform Enterprise installation. An administrator must deploy the agent backend, the Seqera Model Context Protocol (MCP) server, and the web interface, and configure an inference provider. See Install Co-Scientist and Prerequisites.

Get started​

After an administrator deploys Co-Scientist for your installation:

  1. Install the Seqera CLI:

    npm install -g seqera

  2. Log in to Seqera:

    seqera login

  3. Start your first session:

    seqera ai

The CLI must point at your Enterprise deployment rather than Seqera Platform Cloud. See Installation for prerequisites and updates, Authentication for signing in to your installation, and Quickstart to walk through your first session.

What you can do​

Co-Scientist helps across the full pipeline lifecycle, from writing code to running it on Seqera Platform:

Develop pipelines​

Generate Nextflow configurations and pipeline schemas, convert scripts from other languages (WDL, R) to Nextflow, and discover over 1,000 nf-core modules with ready-to-run commands. Build reproducible Wave containers from conda or pip packages without writing a Dockerfile. Real-time language server protocol (LSP) code intelligence detects errors and powers AI navigation across Nextflow, Python, and R files.

Run and debug on Platform​

Launch, monitor, and debug Nextflow workflows with real-time status, logs, and run metrics. Browse cloud storage through data links, manage datasets, generate upload and download URLs, and access reference genomes. Co-Scientist works with the compute environments, datasets, and workspaces your account can already access.

Work your way​

Ask in plain English, or use reusable skills exposed as slash commands in the / palette. Switch between build, plan, and goal modes to match execution, analysis, or long-running tasks. Resume earlier sessions with seqera ai -c, and organize workspace resources into projects using Platform labels.

Learn more​

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