A Review of Hardware Acceleration for Computational Genomics

Abstract

Hardware accelerators are becoming increasingly commonplace in delivering high performance computing solutions at a fraction of the cost of conventional supercomputers and standalone CPU clusters, despite the additional programming effort required to utilize them. This paper provides a survey on the use of hardware accelerators such as FPGAs and GPUs in the area of biological sequence analysis, particularly in the domain of computational genomics. We also survey research on hardware acceleration in response to emerging trends in high-throughput sequencing, and applications enabled by it. We conclude the survey with remarks on how these trends influence the use of hardware acceleration in bioinformatics, and the role of recently developed or soon to be released accelerator technologies.