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Updated: Jul 11, 2025

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
Published on: March 22, 2018
RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures
Xiaoming Xu1, Zekun Yin1, Lifeng Yan1
1School of Software, Shandong University, Jinan, China.
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://github.com/RabbitBio/RabbitKSSD.
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