ArticleGenome biology2021
Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Genetic landscape and evolution of Acinetobacter pittii, an underestimated emerging nosocomial pathogen.Communications biology · 2025Article
- RabbitSketch: a high-performance sketching library for genome analysis.Bioinformatics (Oxford, England) · 2025Article
- Article
- Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii.Nature communications · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Fractional hitting sets for efficient multiset sketching.Algorithms for molecular biology : AMB · 2025Article
- Kssdtree: an interactive Python package for phylogenetic analysis based on sketching technique.Bioinformatics (Oxford, England) · 2024Article
- CAIM: coverage-based analysis for identification of microbiome.Briefings in bioinformatics · 2024Article
- CAIM: Coverage-based Analysis for Identification of Microbiome.bioRxiv : the preprint server for biology · 2024Article
- MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction.Bioinformatics (Oxford, England) · 2024Article
- Distributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century.Nature communications · 2023Article
- 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
- Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis.Genome biology · 2021Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here, we develop k -mer substring space decomposition (Kssd), a sketching technique which is significantly faster and more accurate than current sketching methods. We show that it is the only method that can be used for large-scale dataset comparisons at population resolution on simulated and real data. Using Kssd, we prioritize references for all 1,019,179 bacteria whole genome sequencing (WGS) runs from NCBI Sequence Read Archive and find misidentification or contamination in 6164 of these. Additionally, we analyze WGS and exome runs of samples from the 1000 Genomes Project.
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