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Accelerating Cloud-Based Transcriptomics: Performance Analysis and Optimization of the STAR Aligner Workflow
Piotr Kica, Sabina Licho{\l}ai, Micha{\l} Orzechowski, Maciej Malawski
https://arxiv.org/abs/2506.12611

Accelerating Cloud-Based Transcriptomics: Performance Analysis and Optimization of the STAR Aligner Workflow
In this work, we explore the Transcriptomics Atlas pipeline adapted for cost-efficient and high-throughput computing in the cloud. We propose a scalable, cloud-native architecture designed for running a resource-intensive aligner -- STAR -- and processing tens or hundreds of terabytes of RNA-sequencing data. We implement multiple optimization techniques that give significant execution time and cost reduction. The impact of particular optimizations is measured in medium-scale experiments followe…

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