Massive Parallel Alignment of RNA-seq Reads in Serverless Computing

Abstract

In recent years, the use of Cloud infrastructures for data processing has proven useful, with a computing potential that is not affected by the limitations of a local infrastructure. In this context, Serverless computing is the fastest-growing Cloud service model due to its auto-scaling methodologies, reliability, and fault tolerance. We present a solution based on in-house Serverless infrastructure, which is able to perform large-scale RNA-seq data analysis focused on the mapping of sequencing reads to a reference genome. The main contribution was bringing the computation of genomic data into serverless computing, focusing on RNA-seq read-mapping to a reference genome, as this is the most time-consuming task for some pipelines. The proposed solution handles massive parallel instances to maximize the efficiency in terms of running time. We evaluated the performance of our solution by performing two main tests, both based on the mapping of RNA-seq reads to Human GRCh38. Our experiments demonstrated a reduction of 79.838%, 90.079%, and 96.382%, compared to the local environments with 16, 8, and 4 virtual cores, respectively. Furthermore, serverless limitations were investigated.