Design space exploration of dataflow-based Smith-Waterman FPGA implementations

Abstract

The paper presents the results of design space explorations for the implementation of the Smith-Waterman (S-W) algorithm performing DNA and protein sequences alignment. Both design explorations studies and FPGA implementations are obtained by developing a dynamic dataflow program implementing the algorithm and by direct high-level synthesis (HLS) to FPGA HDL. The main feature of the obtained implementation is a low-latency, pipelinable multistage processing element (PE), providing a substantial decrease in resource utilization and increase in computation throughput when compared to state of the art solutions. The implementation solution is also fully scalable and can be efficiently reconfigured according to the DNA sequence sizes and performance requirements of the system architecture. The implementation solution presented in the paper can efficiently scale up to 250MHz obtaining 14746 Alignments/s using a single S-W core with 4 PEs, and up to 31.8 Mega-Alignments/min using 36 S-W cores on the same FPGA for sequences of 160×100 nucleotides.