High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL

The Smith-Waterman algorithm is widely used in bioinformatics and is often used as a benchmark of FPGA performance. Here we present our highly optimized Smith-Waterman implementation on Intel FPGAs using OpenCL. Our implementation is both faster and more efficient than other current Smith-Waterman implementations, obtaining a theoretical performance of 214 GCUPS. Moreover, due to the streaming, implicit synchronizing nature of our implementation, which streams alignments and places no restrictions on the number of alignments in flight, it achieves 99.8% of this performance in practice, almost three times as fast as previous implementations. The expressiveness of OpenCL results in a significant reduction in lines of code, and in a significant reduction of development time compared to programming in regular hardware description languages.