Esha JoshiEsha Joshi
Aug 14, 2025

Scaling with Seqera: From Prototype to Enterprise-Grade Deployment

Scaling a promising research initiative into an enterprise-grade solution demands a technology foundation that supports both early-stage exploration and the operational standards of global pharma. Leaders face a core challenge: accelerating discovery while ensuring control, scalability, and reliability at every stage.

The reality? Modern scientific research doesn’t just scale up, it scales in every direction: across code, compute, teams, and projects. Today, success isn’t measured by how much data is processed, but by how rapidly teams can adapt, reproduce results, and scale efficiently. Seqera exists to enable this. In this blog, we explore how the Seqera ecosystem empowers R&D leaders to scale innovation, streamline operations, and deliver faster, more reproducible scientific outcomes.

Watch the "Scale with Seqera" talk

Beyond Workflows: Scaling the Full R&D Ecosystem

For pharma R&D, scaling means managing complexity across the broader ecosystem, not just bioinformatics pipelines. As data volumes grow and research becomes more demanding, the challenge lies in building an operation that scales reliably, reproducibly, and securely. True scale relies on alignment across four interconnected axes: code, compute, teams, and projects. These are deeply interdependent: clean code enables reliable projects; projects demand scalable compute; and collaboration across teams must be seamless.

Nextflow is a powerful foundation, but it’s only part of the picture. Seqera brings these capabilities together into a unified, enterprise-ready platform that enables organizations to scale science without sacrificing control.

Scale with Seqera - Code, Compute, Teams, Projects

1. Code: From Legacy Scripts to Production-Ready Pipelines

Why it matters

Scaling science starts with clean, maintainable code. In many R&D environments, legacy scripts evolve into black boxes: difficult to update, audit, or share. This slows progress and increases risk.

How Seqera helps

Seqera equips teams to move faster, reduce dependency on specialists, and ensure pipelines are production-grade from day one:

  • Accelerate time to deployment with AI-assisted pipeline development and faster troubleshooting, powered by Seqera AI and GitHub Copilot in VS Code.
  • Ensure consistency and compliance with real-time code validation through the Nextflow Language Server.
  • Boost team productivity with cloud-based, interactive development in Studios, giving scientists seamless access to data, tools, and compute.
  • Reduce operational overhead by automating environment setup with Wave containers, eliminating time spent configuring tools.

By removing friction from development, Seqera helps teams ship faster, standardize practices, and future-proof their scientific codebase.

"The results were almost immediate. After deploying Seqera Platform, our researchers rapidly became self-sufficient in launching and monitoring pipelines. This has freed up significant technical resources allowing us to focus on high-value tasks." - Director of IT, Arcus Biosciences

Read the Arcus Biosciences Case Study

2. Compute: Scalable Infrastructure Without the Overhead

Why it matters

As research scales, compute bottlenecks become a barrier due to resource limitations but also inefficient provisioning. Teams need infrastructure that’s elastic, governed, and cost-aware.

How Seqera helps

  • Eliminate bottlenecks and delays with on-demand access to cloud compute via Seqera Compute, enabling teams to scale instantly, without infrastructure overhead.
  • Automate enterprise-scale compute environments with Batch Forge—from VPCs to job queues—while maintaining full visibility and cost control.
  • Streamline data access and portability with Fusion, ensuring teams can securely work across environments with data, pipelines, and compute all in one place.
  • Accelerate analysis cycles by taking the analysis to the compute with Studios, enabling immediate, in-context review of pipeline outputs.

Seqera makes enterprise-scale computing as simple as pushing a button, without losing visibility or control.

“Before Seqera, infrastructure setup and management was challenging for us. Now, it just works, automating what used to take hours of manual effort. That's time we get back to focus on science." - Associate Director of Bioinformatics, Bio-Rad Laboratories

Read the Bio-Rad Case Study

3. Teams: Collaboration That Keeps Pace with Science

Why it matters

Scaling teams isn’t just about headcount, it’s about empowering different roles to work together efficiently. Bioinformaticians, data scientists, and wet lab scientists all need access to the right tools and insights without being blocked by technical silos.

How Seqera helps

  • Break down silos with a single platform where all roles have appropriate access to data, pipelines, tools, and results.
  • Improve coordination across global teams with secure, cloud-native environments like Studios and the Platform Launchpad, designed for distributed collaboration.
  • Make results accessible to non-technical users through built-in visualizations with MultiQC,shared interactive sessions and one-click access to cloud-hosted data.
  • Reduce turnaround times by giving every team the tools they need—when and where they need them—without reliance on local setups or handovers.
“We were able to reduce pipeline costs by 70% over 2 years, lowering the cost per sample and enabling more researchers to achieve results quickly and at industry-leading cost.” - VP Computational Biology & Analytics, BioSkryb Genomics

Read the BioSkryb Genomics Case Study

4. Projects: Visibility, Reproducibility, and Control at Scale

Why it matters

At the enterprise level, success is about managing dozens of concurrent projects with consistency and traceability. That means knowing what ran, how, and why it worked (or didn’t).

How Seqera helps

  • Ensure traceability and auditability for every pipeline run, with full visibility into inputs, parameters, compute, and outcomes.
  • Resolve failures faster using interactive debugging in Studios, reducing the troubleshooting cycle from hours to minutes.
  • Standardize execution across teams and sites with reproducible containers and automated run environments via Wave and the Platform API or CLI.
  • Confidently manage project sprawl with built-in governance, versioning, and orchestration - all in a unified platform designed for scale

Whether it’s a single analysis or a global initiative, Seqera helps teams deliver results they can stand behind.

"Seqera has made it much easier to track pipeline execution and organize datasets. By maintaining a searchable run history, Seqera Platform gives us visibility to track prior pipeline runs – a critical feature for ensuring reproducibility and auditability." - Director of Data Platforms, Tessera Therapeutics

Read the Tessera Therapeutics Case Study

Conclusion: Scale Without Compromise

As data volumes grow, teams expand, and scientific demands accelerate, your ability to scale should be a competitive advantage, not a constraint. But too often, growth brings fragmentation, friction, and lost time.

Seqera offers a unified platform purpose-built to meet the needs of enterprise R&D, bringing together code, compute, teams, and projects into a single ecosystem. The result? Faster development, smoother collaboration, and fully reproducible science at scale.

Your science should not be slowed down as your data, workflows, and teams get bigger. Seqera is here to help and welcome you to bioinformatics without bottlenecks.

Reach out to find out more