ArticleGenome biology2023
RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Use of proximity ligation shotgun metagenomics to investigate the dynamics of plasmids and bacteriophages in the gut microbiome following fecal microbiota transplantation.Gut microbes · 2025Article
- Article
- Comparative genomics and transcriptomics of theResearch square · 2025Article
- skDER and CiDDER: two scalable approaches for microbial genome dereplication.Microbial genomics · 2025Article
- Plasmids, prophages, and defense systems are depleted from plant microbiota genomes.Genome biology · 2025Article
- RabbitSketch: a high-performance sketching library for genome analysis.Bioinformatics (Oxford, England) · 2025Article
- Genomic revisitation and reclassification of the genusmSphere · 2024Article
- DistinctFrontiers in microbiomes · 2024Article
- RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures.Bioinformatics (Oxford, England) · 2023Article
- RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches.Genome biology · 2023Article
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Authors and funding
9 authors.
Funding
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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 from RefSeq, 455 GB in FASTA format, can be clustered within less than 6 min and 1,009,738 GenBank assembled bacterial genomes, 4.0 TB in FASTA format, within only 34 min on a 128-core workstation. Our results further identify 1269 redundant genomes, with identical nucleotide content, in the RefSeq bacterial genomes database.
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