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RabbitSketch: a high-performance sketching library for genome analysis.

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Názov: RabbitSketch: a high-performance sketching library for genome analysis.
Autori: Zhang, Tong, Yin, Zekun, Xu, Xiaoming, Yan, Lifeng, Zhu, Fangjin, Duan, Xiaohui, Schmidt, Bertil, Liu, Weiguo
Zdroj: Bioinformatics; May2025, Vol. 41 Issue 5, p1-4, 4p
Predmety: GENOMICS, C++, ALGORITHMS, GENOMES, DOCUMENTATION
Abstrakt: Summary We present RabbitSketch, a highly optimized library of sketching algorithms such as MinHash, OrderMinHash, and HyperLogLog that can exploit the power of modern multi-core CPUs. It provides significant speedups compared to existing implementations, ranging from 2.30× to 49.55×, as well as flexible and easy-to-use interfaces for both Python and C++. As a result, the similarity analysis of 455GB genomic data can be completed in only 5 minutes using RabbitSketch with merely 20 lines of Python code. As a case study, we enhanced RabbitTClust by integrating RabbitSketch's Kssd algorithm, resulting in a 1.54× speedup with no loss in accuracy. Availability and implementation RabbitSketch is available at https://github.com/RabbitBio/RabbitSketch with an archived version at Zenodo: https://doi.org/10.5281/zenodo.14903962. Detailed API documentation is available at https://rabbitsketch.readthedocs.io/en/latest. [ABSTRACT FROM AUTHOR]
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Databáza: Complementary Index
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Abstrakt:Summary We present RabbitSketch, a highly optimized library of sketching algorithms such as MinHash, OrderMinHash, and HyperLogLog that can exploit the power of modern multi-core CPUs. It provides significant speedups compared to existing implementations, ranging from 2.30× to 49.55×, as well as flexible and easy-to-use interfaces for both Python and C++. As a result, the similarity analysis of 455GB genomic data can be completed in only 5 minutes using RabbitSketch with merely 20 lines of Python code. As a case study, we enhanced RabbitTClust by integrating RabbitSketch's Kssd algorithm, resulting in a 1.54× speedup with no loss in accuracy. Availability and implementation RabbitSketch is available at https://github.com/RabbitBio/RabbitSketch with an archived version at Zenodo: https://doi.org/10.5281/zenodo.14903962. Detailed API documentation is available at https://rabbitsketch.readthedocs.io/en/latest. [ABSTRACT FROM AUTHOR]
ISSN:13674803
DOI:10.1093/bioinformatics/btaf249