Accelerating Genome Assembly Using Hard Embedded Blocks in FPGAs

Modern FPGAs consist of a number of Hard Embedded Blocks (HEBs) like BRAMs, DSPs, PCI controllers, etc. for performing specialized operations/functions. This helps in developing efficient architectures for accelerating compute intensive kernels. Computational genomics is a fairly recent domain which helps in the understanding of the biological properties of an organism with applications in medicine, evolutionary biology and social sciences. A key problem in this research domain is the assembly of DNA sequences obtained from sequencing machines. Next Generation DNA Sequencing (NGS) technologies generate a large number of short fragments (sequences) of fixed length known as reads, which are a part of the genome sequence being assembled. It is computationally very time consuming to assemble these short reads to form the genome sequence purely with software. FPGAs have been effectively used to build accelerators to speed up the computation process. In this paper, we propose HEBs to accelerate the genome assembly process. We show 20% increase in speedups using FPGAs with HEBs over existing FPGA implementation. Speedups of up-to 11x can be obtained over Velvet [1] which is a commonly used software implementation.