RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures

Abstract

Summary We propose RabbitKSSD, a high-speed genome distance estimation tool. Specifically, we leverage load-balanced task partitioning, fast I/O, efficient intermediate result accesses, and high-performance data structures to improve overall efficiency. Our performance evaluation demonstrates that RabbitKSSD achieves speedups ranging from 5.7x to 19.8x over Kssd for the time-consuming sketch generation and distance computation on commonly used workstations. In addition, it significantly outperforms Mash, BinDash, and Dashing2. Moreover, RabbitKSSD can efficiently perform all-vs-all distance computation for all RefSeq complete bacterial genomes (455 GB in FASTA format) in just 2 minutes on a 64-core workstation. Availability RabbitKSSD is available at https://github.com/RabbitBio/RabbitKSSD. Supplementary information Supplementary data are available at Bioinformatics online.