Kunwoo Park: CloudMapper: A Pay-as-you-go Solution for Accelerating Genomics Sequence Alignment Using Public Clouds

 CloudMapper: A Pay-as-you-go Solution for Accelerating Genomics Sequence Alignment Using Public Clouds

Abstract: Single-cell RNA sequencing (scRNA-seq) alignment remains a computational bottleneck in bioinformatics data analysis. As datasets grow in size and complexity, traditional alignment tools, such as CellRanger, face significant limitations, often requiring hours or even days. Furthermore, setting up the necessary infrastructure frequently demands familiarity with complex tools like Slurm, creating a barrier for researchers without cluster management expertise. To address these challenges, we introduce CloudMapper, a pay-as-you-go solution that simplifies and accelerates scRNA-seq alignment through scalable public cloud resources. Built on the Texera platform, CloudMapper allows researchers to launch and manage clusters on cloud providers like AWS via an intuitive web interface, enabling parallel processing of large scRNA-seq datasets. By automating infrastructure setup and providing streamlined resource options, CloudMapper offers bioinformaticians flexible tools to balance cost and performance, significantly reducing alignment time and technical overhead. In this talk, we’ll explore CloudMapper’s problem-centered design, architectural framework, and user experience tailored for bioinformaticians. We’ll also discuss ongoing research challenges, such as minimizing manual configuration for non-expert users, optimizing resource pre-provisioning to reduce cluster launch times, and future plans to expand CloudMapper’s capabilities beyond RNA alignment to broader bioinformatics and data-processing tasks.

Bio: Kunwoo Park is a second-year Ph.D. student in the Computer Science Department at UC Irvine, with research interests in data systems and big data a