FastBWA: Practical and Cost-Efficient Genome Sequence Alignment Pipeline

Sequence alignment is a fundamental and often time-consuming step in genomic data analysis. Typically, it adheres to the seed-and-extension paradigm and numerous accelerator-based approaches have been proposed to optimize either of the kernels. However, these approaches often increase costs and contribute minimally to the overall alignment process. To address this, we have designed an optimized full pipeline, FastBWA, which seeks to enhance performance while keeping costs low and explores the potential of CPU computing resources. Our implementation demonstrates that FastBWA achieves up to 2.5× and 1.8× in end-to-end alignment throughput compared to BWA-MEM and its newer version, BWA-MEM2.