What’s New at Seqera: GxP-Aligned Bioinformatics, Expanded Data Connections, AI Integrations, and More

I began today's Nextflow Summit talking about our vision to make scientists' lives simpler, one pipeline at a time. The same platform, but better suited to bioinformatics in 2025. Every product update we’ve announced today builds on this foundation, moving us through the complete journey from scientific infrastructure, through innovation and velocity. From GxP-aligned pipeline versioning and in-platform data exploration on HPC, to AI in Platform and our new MCP Server, here’s the latest Seqera updates you won’t want to miss.

Scientific Infrastructure - From R&D to GxP

Our platform improvements start with the fundamentals that every scientist needs daily: responsive design, better UX, and enhanced troubleshooting capabilities. But we're also entering a new era for reproducible workflows, extending these core improvements to meet the rigorous demands of regulated environments. Regulated industries require platforms that meet stringent compliance standards for data integrity, audit trails, and reproducible analysis. Seqera now delivers enterprise-grade capabilities specifically aligned with GxP and regulatory requirements.

Pipeline Run Details Improvements

Our platform improvements start with the fundamentals that every scientist needs daily: responsive design, better UX, and enhanced troubleshooting capabilities. Following user feedback, we've enhanced the Pipelines Run Details page with new troubleshooting capabilities. Updates include simplified log collection for errored runs that allows downloading relevant support logs as zipped files, eliminating manual log collection, and enhanced UI design that improves consistency and usability across devices. These updates streamline the debugging process while maintaining familiar user flows.

Pipeline Versioning

Seqera now provides pipeline versioning with automatic snapshots of every configuration change, named version management, and role-based controls. Pipeline owners can set default versions, control visibility, and edit sensitive settings, while launch users can only run approved defaults and modify allowed fields. Each pipeline run is tied to an exact version with stored checksums, ensuring complete reproducibility and audit trails aligned with GxP requirements. This eliminates scattered pipeline copies and provides the traceability required for FDA/EMEA submissions and regulatory audits.

Fine-Grained Authorization

Seqera now allows you to augment your existing roles (Owner, Launch, View, etc.) with custom ones that mirror your organizational structure and security/compliance requirements. You can now create roles on-demand, assign granular permissions, and manage access changes instantly through self-service controls, all without vendor support tickets or system downtime. This enterprise-tier capability integrates with your existing SSO while maintaining complete audit logs for compliance reviews. Stop choosing between security risks and productivity blocks when standard permission models don't fit your teams.

Scientific Innovation - Data Improvements

Biology is generating increasingly complex data types—single-cell, spatial omics, long-read sequencing, and metagenomics—from diverse sources including object storage, public datasets, LIMS, Databricks, and Snowflake. Our latest updates help you manage this complexity with enhanced data exploration, improved data management, streamlined development environments, and expanded compute options across your entire ecosystem

Data Explorer Support for S3-Compatible Storage

Data Explorer enables researchers to securely connect, browse, and interact directly with remote data repositories through intuitive, visual navigation and point-and-click selection within Seqera Platform. We’ve extended Data Explorer beyond the big three (AWS, GCP, Azure) hyperscale cloud object storage providers to work seamlessly with any S3-compatible storage (cloud and on-premise HPC environments). You can now explore, preview, and select data adjacent to your object storage, without switching tools or manually migrated files. This creates a truly unified bioinformatics experience where your data interactions and compute are centralized in a single platform.

Datasets Improvements

Datasets in Seqera are CSV and TSV files stored in workspaces that serve as pipeline inputs to simplify data management, minimize user errors, and facilitate reproducible workflows. We have completely rebuilt Datasets with modern design components and enhanced functionality, including improved metadata handling, advanced filtering by metadata values, dataset labeling, and show/hide controls. Users can also now track pipeline runs using specific datasets through one-click views, while enhanced preview and pagination make exploration more intuitive.

Studios Git-Provider Integration

Studios, Seqera’s interactive analysis feature, already allows you to define and deploy your preferred custom applications adjacent to your data. Now, Studios integrates directly with Git-providers (including GitHub, GitLab, Bitbucket, and Azure DevOps), connecting directly to your existing public or private code repositories to streamline environment management. Simply paste your Git-provider repository path, select a valid revision (commit ID, tag, or branch name) and Seqera automatically pulls your session configuration, any customizations or augmentations, and clones your repository contents into the new Studio session. You can also now specify a raw Dockerfile in your confiugration, and Studios automatically compiles this into an analysis environment. This improvement eliminates manual tracking of session configurations and custom environment file uploads, keeps your configuration code centralized, standardized, and secure, and makes custom analysis environments significantly faster to deploy.

Azure Cloud Compute Environment

We have introduced a new, simplified compute environment (Azure Cloud) designed for faster Nextflow pipeline launch and runs and Studios environment creation for customers with Azure tenants. This new virtual machine-based compute environment addresses common Batch service pain points such as long launch delays, complex setup, and allocation constraints, and brings Azure in line with the new AWS Cloud and GCP Cloud compute environments released earlier this year.

Scientific Velocity - New Paradigm of Agentic Research

AI could be humanity's most important invention. We're channeling it toward improving human and planetary health. Today, preclinical research and drug discovery usually take three to six years using traditional methods. The future we're building? Turning this timeline from years into months. To achieve this, we need the core fundamentals: compute, workload orchestration, data, and the right tools, models, pipelines, and development environments working together seamlessly.

Seqera AI in Platform

Seqera AI, the bioinformatics agent for the R&D lifecycle, now integrates directly with Seqera Platform, bringing conversational AI capabilities to your secure bioinformatics environment. This enables scientists to debug pipelines, modify parameters, and launch runs through natural language without switching tools or interfaces. Your existing security and compliance safeguards remain fully intact. Through the Seqera AI chat interface you can now:

• Execute pipelines: Run popular open-source pipelines on your data
• Debug failures: Get intelligent assistance troubleshooting failed runs
• Generate datasheets: Create analysis summaries and documentation
• Enable wet-lab access: Let bench scientists interact with computational results

Seqera MCP Server

Transform your AI assistant into a powerful control center for Seqera Platform. The new Seqera MCP server enables seamless integration between Seqera Platform and any MCP-compatible AI tool, including Claude, VS Code Copilot, and Cursor. With full Platform authentication and SSO integration, your preferred AI tool becomes a unified workspace for computational biology, transforming an isolated compute environment into a first-class citizen of today's ever-expanding AI ecosystem.

Seqera Compute Free Tier

Seqera Compute (our managed, optimized compute service) enables you to run Nextflow pipelines and interactive analysis at scale without the hassle of setting up your own compute environment. Today, we're excited to announce a free tier offering that provides new users with access to compute to start running bioinformatics workloads immediately. Everyone who signs up to Seqera Cloud with an organizational email now gets $100 of free compute—complete with pipelines and sample data that are already connected. With no coordination with IT teams or cloud environment configuration required, this gets you from account creation to running pipelines in under a minute, with the flexibility to choose from example template workflows to get started, or the option to bring your own.

The Complete Journey - From Infrastructure to Innovation to Velocity

What we've shared today represents the complete journey from solid scientific infrastructure through data innovation to AI-powered velocity. Each layer builds on the last, creating the foundation needed to turn years-long research cycles into months. Whether you're debugging a pipeline, exploring complex datasets, or leveraging AI for breakthrough discoveries, these updates ensure Seqera delivers both the usability scientists need daily and the transformative capabilities that will define the future of computational biology.