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 5.7× to 19.8× 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 min on a 64-core workstation.

Availability and implementation

RabbitKSSD is available at https://g

SUBMITTER: Xu X 

PROVIDER: S-EPMC10681859 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature