RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 37971961.
- Also identified by DOI 10.1093/bioinformatics/btad695 and PMC identifier 10681859.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. RabbitKSSD is available at https://github.com/RabbitBio/RabbitKSSD.
Medical subject headings
- Genome, Bacterial
- Software