On the Genome Sequence Alignment FPGA Acceleration via KSW2z

Abstract

Pairwise sequence alignment is a fundamental step for many genomics and molecular biology applications. Given the quadratic time complexity of alignment algorithms, the community demands innovative, fast, and efficient techniques to perform this task. Furthermore, general-purpose architectures lack the necessary performance to address the computational load of these algorithms. In this context, we present the first open-source FPGA implementation of the popular KSW2z algorithm employed by minimap2. Our design also implements the $Z- \mathbf{drop}$ heuristic and banded alignment as the original software to further reduce the processing time if needed. The proposed multi-core accelerator achieves up to $\mathbf{7.70}\times$ improvement in speedup and $\mathbf{20.07}\times$ in energy efficiency compared to the multi-threaded software implementation run on a Xeon Platinum 8167M processor.