Seqera AI

Seqera AI is a bioinformatics AI agent purpose-built for the full R&D lifecycle, enabling researchers and data scientists to generate, validate, and execute production-ready Nextflow pipelines entirely within a single conversational interface. Designed for both experienced bioinformaticians and wet lab scientists with limited coding expertise, Seqera AI brings together pipeline development, debugging, execution, and results analysis in one unified, AI-powered experience.

Built on deep knowledge of Nextflow DSL2, nf-core standards, and bioinformatics best practices, Seqera AI accelerates the path from experimental data to actionable insights by eliminating context switching and reducing the technical barriers that slow down research productivity.

Core Capabilities

• Pipeline Development: Interactively explore, debug, and generate entire Nextflow pipelines from scratch following nf-core best practices. Load public examples or connect your own pipeline via a GitHub URL for instant, contextual understanding of your workflow structure.
• Code Conversion: Transform existing bash, CWL, and WDL scripts into production-ready DSL2 Nextflow pipelines with high accuracy, including support for converting legacy DSL1 pipelines to DSL2.
• Built-in Nextflow Expertise: Purpose-built AI understanding of Nextflow DSL2, nf-core standards, and bioinformatics best practices ensures generated code meets quality and reproducibility requirements.
• Smart Resource Optimization: Analyze run history to identify performance bottlenecks, suggest optimal resource settings, and auto-configure pipelines based on past execution performance.
• Direct Platform Integration: Debug failed runs, modify parameters, launch pipelines, and browse S3 data structures directly through AI chat with full access to Seqera Platform environments and execution history.
• Chat-to-Execution: Execute any Launchpad pipeline directly from the chat interface without switching tools, with automatic configuration and execution handling.
• Smart Dataset Discovery: Find relevant public datasets through SRA search and automatically match data to appropriate pipelines for your experiments.
• Interactive Results Analysis: Analyze MultiQC reports, interpret scientific results, and explore data structures through AI that understands experimental context, including AI-generated summaries of MultiQC analysis results with interactive chat for deeper exploration.

Deployment and Interface Options

• Seqera AI Chat: A web-based conversational interface for pipeline building, debugging, execution, and results interpretation.
• Seqera AI CLI: A terminal-native assistant that brings context-aware AI directly to your command-line Nextflow development environment, with full access to your Platform workspace and local development environment.
• Seqera MCP: Connect to the Model Context Protocol for additional integration flexibility.

Key Workflow Use Cases

1. Generate a new Nextflow pipeline for analyses such as RNA-seq or variant calling from a natural language description.
2. Load an existing pipeline from a GitHub URL and receive contextual explanations and optimization suggestions.
3. Debug a failed workflow run by providing error messages or run identifiers and receiving guided resolution steps.
4. Search SRA for relevant public datasets and match them to suitable pipelines automatically.
5. Launch pipelines on Seqera Platform directly from chat, adjusting parameters as needed.
6. Review MultiQC reports through AI-generated summaries and interactive follow-up questions.

Seqera AI integrates with Seqera Platform and Nextflow, and is validated by scientists with comprehensive understanding of bioinformatics tools and the broader scientific community. By unifying discovery, development, execution, and analysis in a single AI-powered interface, Seqera AI democratizes bioinformatics and enables teams to focus on scientific discovery rather than technical implementation challenges.