Parallel Generalized Suffix Tree Construction for Genomic Data

Abstract

After a decade of digitization and technological advancements, we have an abundance of usable genomic data, which provide unique insights into our well-being. However, such datasets are large in volume, and retrieving meaningful information from them is often challenging. Hence, different indexing techniques and data structures have been proposed to handle such a massive scale of data. We utilize one such technique: Generalized Suffix Tree (GST). In this paper, we introduce an efficient parallel generalized suffix tree construction algorithm that is scalable for arbitrary genomic datasets. Our construction mechanism employs shared and distributed memory architecture collectively while not posing any fixed, prior memory requirement as it uses external memory (disks). Our experimental results show that our proposed architecture offers around 4-times speedup with respect to the sequential algorithm with only 16 parallel processors. The experiments on different datasets and parameters also exhibit the scalability of the execution time. In addition, we utilize different string queries and demonstrate their execution time on such tree structure, illustrating the efficacy and usability of GST for genomic data.