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bioRxiv · 10.1101/2022.10.13.512052

RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches

Xu, X.·Yin, Z.·Yan, L.·Zhang, H.·Xu, B.·Wei, Y.·Niu, B.·Schmidt, B.·Liu, W.
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Abstract

We present RabbitTClust, a fast and memory-efficient genome clustering tool based on sketch-based distance estimation. Our approach enables efficient processing of large-scale datasets by combining dimensionality reduction techniques with streaming and parallelization on modern multi-core platforms. 113,674 complete bacterial genome sequences (RefSeq: 455 GB in FASTA format) can be clustered within less than 6 minutes and 1,009,738 GenBank assembled bacterial genomes (4.0 TB in FASTA format) within only 34 minutes on a 128-core workstation. Our results further identify 1,269 repetitive genomes (identical nucleotide content) in RefSeq bacterial genomes.

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Xu, X., Yin, Z., Yan, L., Zhang, H., Xu, B., Wei, Y., Niu, B., Schmidt, B., Liu, W.. 2022-10-17. RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches. https://doi.org/10.1101/2022.10.13.512052

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