Strand Life Sciences Scaled Sample Throughput by 35x by Migrating Pipelines to Nextflow and Deploying on Seqera

Aim

Standardize and optimize data pipelines for genomics, biomanufacturing QC, and development to accelerate discovery and support diverse client needs across pharma, diagnostics, and precision medicine.

Challenges

One of the primary challenges Strand Life Sciences faced was inefficient computational resource management during large-scale genomic data processing. Their legacy system provided limited CPU and memory monitoring, creating inefficiencies that increased turnaround times and costs. Additionally, handling I/O bottlenecks with massive datasets posed significant difficulties. Transferring data exceeding 100 terabytes from cloud storage to compute servers could take several days, severely limiting throughput.

Beyond resource management and throughput limitations, Strand faced operational complexity from fragmented systems. Traditional approaches maintained separate workflows for QC, alignment, and variant calling, creating complex frameworks requiring manual oversight. Legacy workflows required individual configuration for each compute environment, slowing deployment across local, HPC, and cloud platforms. They also offered poor flexibility for resuming interrupted runs, making restarts time-consuming, and maintaining comprehensive logs was difficult, creating reproducibility challenges across projects.

Solution

• Nextflow: Modernized workflow architecture with reproducible, scalable pipelines that standardized processes across teams and environments.
• nf-core: Accelerated development with ready-to-use community modules and established best practices for robust pipeline construction.
• Seqera: Centralized workflow management with real-time visibility, dynamic scaling, and dramatic performance improvements in runtime and sample throughput.

Results

As client projects scaled in complexity and volume, Strand undertook a strategic initiative to standardize their bioinformatics operations and modernize their workflow infrastructure. By migrating their legacy pipelines to Nextflow and deploying on Seqera Platform, Strand enhanced scalability, reproducibility, and operational efficiency. The result was a 55% reduction in workflow execution time, 35x increase in sample throughput, and 66% reduction in total costs. These enhancements standardized code development and established robust, reliable computational pipelines that now serve as the foundation for future genomic analysis workflows across diverse client environments and research applications at Strand.

Feature image credit: https://quadriacapital.com/portfolio/exits/strand-life-sciences