Cost per sample? Try cost per attempt
This article is aimed at bioinformatics platform leads, ML infrastructure engineers, and genomics budget owners who are now running GPU-accelerated workflows in the cloud. It's about a hidden cost problem that almost every genomics infrastructure team is paying for — and very few are actively measuring. The observations here are specific to short-read sequencing workflows, which remain the dominant data type in production genomics environments.
Short-read sequencing pipelines, standard in next-generation sequencing (NGS) workflows, used to be CPU-heavy. You'd run them on a cluster, they'd grind through alignment and variant calling over hours, and the bottleneck was CPU throughput. GPU acceleration wasn't the story.
That has changed. AI-driven variant calling, GPU-accelerated alignment tools like Parabricks, and deep learning models running on top of sequencing data have all moved toward the GPU, which means teams are managing serious GPU infrastructure for the first time.
The cost model that comes with GPU...
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