Streamlining Bioinformatics at Bio-Rad with Fusion: Faster Workflows, Cost-Efficiency, and Simplified Infrastructure

Aim

Bring products to market that empower customers to make groundbreaking discoveries and improve lives, in addition to creating new knowledge that impacts our understanding of biology and healthcare.

Challenges

Bio-Rad Laboratories faced ongoing challenges in maintaining organization and consistency in their bioinformatics workflows. Pipelines for multiple experimental assays (single-cell ATAC-seq, RNA-seq) were housed in single repositories, leading to branching, divergence and development inefficiencies. Despite efforts to consolidate these workflows, the rapid pace of research continually introduced fragmentation. Additionally, the high cost of sequencing coupled with the urgency for fast scientific insights often forced prioritization of speed over structured workflow design. This trade-off resulted in growing technical debt, requiring continuous restructuring efforts to maintain consistency and reliability across bioinformatics operations.

Before adopting Fusion, Bio-Rad relied on EBS auto-scaling on AWS, which, while functional, was slow and overseen manually. The absence of a centralized infrastructure team led to inconsistent setups, placing the burden of cloud resource management on scientists with limited infrastructure expertise. This inefficiency not only increased operational costs but also made scaling single-cell data analysis more challenging. As data demands grew, it became clear that a faster, more cost-effective, and automated solution was essential to streamline workflow execution and optimize cloud resource utilization.

Solution

• Nextflow: Enabled the creation of scalable bioinformatic pipelines that are highly reproducible and can be deployed across various infrastructure and environments.
• Seqera: Ability for scientists and engineers to analyze data directly on their own cloud infrastructure, and providing organization-wide centralized visibility of pipeline configurations and executions.
• Fusion: Accelerated the time-to-results and reduced the infrastructure burden by eliminating the dependency on EBS volume sizing and cleanup, typically necessary for AWS Batch.

Results

Using Fusion and Seqera Platform, Bio-Rad has transformed its bioinformatics workflows, improving scalability, efficiency, and cost-effectiveness. By automating infrastructure setup and optimizing data access, they were able to reduce data processing times, eliminate storage inefficiencies, and save on cloud expenses. These advancements freed researchers from manual setup and resource management, allowing them to focus on innovation and scientific discovery.

Feature image credit: https://www.bio-rad.com/