Case Study: UC Santa Cruz Genomics Institute achieves rapid, cost-effective large-scale RNA-seq analysis with Amazon Web Services

UC Santa Cruz Genomics Institute - Customer Case Study

The UC Santa Cruz Genomics Institute, including its Treehouse Childhood Cancer Initiative, needed to reprocess large, inconsistent RNA‑seq data sets so clinicians could use genomic analyses to guide cancer treatment. Limited in‑house compute, varied processing pipelines, and slow data transfer meant reanalysis could take months—far too long when clinicians often have only days to act.

The lab developed the open‑source Toil workflow and ran it on AWS (EC2, S3, Spot Instances, ECS), reprocessing ~20,000 RNA‑seq samples across 32,000 cores in under four days instead of months. This eliminated transfer bottlenecks, delivered results to clinical partners far faster, and reduced estimated costs from ~$800,000 to $26,000, enabling quicker, more affordable genomic analyses with direct patient impact.

UC Santa Cruz Genomics Institute

Benedict Paten

Director, Computational Genomics Lab