Faster and Cheaper: Pushing the Sequence Alignment Throughput with Commercial CPUs

This paper proposes FastAlign, a faster, cheaper, and practical end-to-end solution for sequence alignment using commercial CPUs. It introduces two key innovations: a multi-stage seeding algorithm that improves search performance while maintaining low memory consumption, and an intra-query parallel seed-extension algorithm that eliminates redundancy and increases SIMD utilization. Evaluation results show that FastAlign achieves 2.27× ∼ 3.28× throughput speedup and 2.54× ∼ 5.65× cost reduction compared to state-of-the-art CPU and GPU baselines while guaranteeing 100% identical output to the de facto software BWA-MEM. FastAlign is open-sourced at https://github.com/zzhofict/BWA-FastAlign.git.