ArticleBioinformatics (Oxford, England)2023
RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- RabbitSketch: a high-performance sketching library for genome analysis.Bioinformatics (Oxford, England) · 2025Article
- Structural Insights into Cold-Active Lipase from Glaciozyma antarctica PI12: Alphafold2 Prediction and Molecular Dynamics Simulation.Journal of molecular evolution · 2024Article
- Article
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7 authors.
Funding
Abstract
summaryWe 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://github.com/RabbitBio/RabbitKSSD.
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Registered trials
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