GPU Acceleration of Advanced k-mer Counting for Computational Genomics

摘要

k-mer counting is a popular pre-processing step in many bioinformatic algorithms. KMC2 is one of the most popular tools for k-mer counting. In this work, we leverage the computational power of the GPU to accelerate KMC2. Our goal is to reduce the overall runtime of many genome analysis tasks that use k-mer counting as an essential step. Compared to KMC2 running on a single CPU thread, our implementation using the GPU achieved$mathbf{4.03x}$speedup when using one CPU thread, and$mathbf{5.88x}$speedup when using four CPU threads. This speedup is significant because accelerating k-mer counting is challenging due to reasons like serialized portions of code and overhead of disk operations.