RabbitSketch: a high-performance sketching library for genome analysis.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 40286290.
- Also identified by DOI 10.1093/bioinformatics/btaf249 and PMC identifier 12054975.
- 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 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. RabbitSketch is available at https://github.com/RabbitBio/RabbitSketch with an archived version at Zenodo: https://doi.org/10.5281/zenodo.14903962.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.
Medical subject headings
- Software
- Genomics
- Algorithms
- Genome