Gigabyte-scale alignment of biological sequences: A case study of IO bandwidth reconfiguration for FPGA acceleration

We expose the implementation challenges to sustaining acceleration speedups on FPGAs as the size of the data set to be processed scales. We examine the implementation of an FPGA platform for the processing of gigabyte scale biological sequences, and illustrate the significant design changes that must be made to achieve a successful implementation. In doing so, we demonstrate that conventional accelerator architecture design choices that focus on throughput speedup, in isolation of system level IO bandwidth feasibility, cannot sustain their throughput levels as the input data set scales. This is shown to be primarily due to currently unavailable high-bandwidth large-scale data storage and retrieval for FPGAs. As a solution to this problem, we propose a general FPGA based IO infrastructure to utilize high bandwidth hard-drive storage options, as means to achieving sustained throughput in the face of large data.