The AI revolution is reshaping how we interact with computational infrastructure. We recently announced the Seqera AI integration in platform, our purpose-built bioinformatics AI that can directly execute, debug, and launch workflows within Seqera Platform. Today, we're taking the next decisive step forward by opening Seqera to the entire AI ecosystem through our new Seqera MCP server. Fully integrated with Seqera single sign on (SSO), you can make your preferred AI tool (e.g. Claude AI, VS Code Copilot, Cursor) your new control center for Seqera.
We envision a future where your computational workflows are accessible through any AI tool you choose. The Seqera MCP server doesn't just connect systems; it opens our entire platform to the rapidly expanding universe of AI agents, making Seqera a first-class citizen in the AI-driven computational landscape.
The Challenge: Computational Silos
Even the most sophisticated AI assistants operate in isolation. They can write functional code, suggest optimizations, and debug complex issues, but they lack the context of cloud infrastructure, pipeline run history, and data. This disconnect creates friction. Bioinformaticians find themselves constantly switching between AI coding assistants and external interfaces to bridge the gap between their AI tools and what is happening in their cloud.
MCP: The Universal Language for AI Tools
The MCP protocol, developed by Anthropic, serves as the universal gateway that opens computational platforms to any AI tool. Think of MCP as an adapter that breaks down the walls between AI assistants and external services. Instead of computational platforms remaining isolated from the AI ecosystem, MCP creates a standardized protocol that allows any AI tool to access and interact with your infrastructure: a single interface enabling seamless interoperability across your entire toolchain.
Seqera MCP: Opening Our Platform to Your AI Ecosystem
With the Seqera MCP server, we're opening Seqera to work seamlessly with any MCP-compatible AI tool—Claude Desktop, GitHub Copilot, Cursor, VS Code, and the growing ecosystem of AI agents. This isn't just an integration; it's our commitment to ensuring Seqera evolves with the AI-first future of computational science. Your workflows, data, and computational resources are no longer confined to a single interface. They're now accessible through the AI tools you’re already using, the ones you're discovering, and the ones that haven't been built yet.
Claude: Pipeline Troubleshooting
Ask Claude natural language questions about your Seqera workflows and get detailed insights through interactive conversation. For example: “What went wrong on my last run in my Seqera workspace?”.
Cursor: Explore Pipeline Runs
Access Seqera directly from your Cursor IDE to explore your Seqera run history. Ask questions like: “Tell me about my latest runs on Seqera?”.
VS Code GitHub Copilot: Debug Pipelines
Get intelligent troubleshooting assistance with contextual suggestions for workflow failures, without leaving VS Code. For example, you can ask: “What went wrong with this run?”.
Free Access Through Seqera
We’re making the Seqera MCP server freely available to all Seqera users, fully integrated with your existing Platform SSO. This approach ensures access while maintaining the security and user management you already rely on. Our free MCP server provides:
- Zero friction access - No additional authentication or setup required beyond your existing Platform credentials
- Enterprise-grade security - Full SSO integration means your access controls and permissions carry through to AI interactions
- Immediate availability - Start using any MCP-compatible AI tool with Seqera in minutes
- Unified user experience - Your Platform identity, permissions, and workspace access work consistently across all AI tools
By opening our platform through standardized protocols, we're contributing to an ecosystem where bioinformatics platforms and AI tools work together seamlessly, while ensuring security and governance requirements remain intact.
More Than Just Integration
The Seqera MCP is more than just integration, it’s our vision for how bioinformatics platforms should evolve in the AI era. MCP transforms Seqera from a bioinformatics stack into an intelligent layer that any tool in the growing AI ecosystem can leverage. Consider the implications:
- AI-Native Access: Seqera becomes natively accessible to any current or future AI tool
- Context-Aware AI: Your AI assistants now understand your actual computational environment, not just generic code
- Tool Freedom: Use your preferred AI interface while maintaining full access to Seqera capabilities.
- Future-Ready: As new AI tools emerge, you can immediately access Seqera through MCP
Getting Started: Your Workflows, Your Way
The Seqera MCP server works with any MCP-compatible AI tool. Whether you're already using Claude Desktop for research planning, GitHub Copilot for development, or exploring new AI-powered workflows, adding Seqera integration takes just minutes. Your computational workflows become as accessible as asking a question, and your preferred AI interface becomes your new control center for Seqera.