ArticleGenome research2023
Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2.
Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- Hash functions in nucleotide sequence analysis.Genome research · 2026Review
- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.Research square · 2025Article
- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.bioRxiv : the preprint server for biology · 2025Article
- Mumemto: efficient maximal matching across pangenomes.Genome biology · 2025Article
- RabbitSketch: a high-performance sketching library for genome analysis.Bioinformatics (Oxford, England) · 2025Article
- Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain.Nature microbiology · 2025Article
- EvANI benchmarking workflow for evolutionary distance estimation.Briefings in bioinformatics · 2025Article
- EvANI benchmarking workflow for evolutionary distance estimation.bioRxiv : the preprint server for biology · 2025Article
- Combining DNA and protein alignments to improve genome annotation with LiftOn.Genome research · 2025Article
- Review
- Fractional hitting sets for efficient multiset sketching.Algorithms for molecular biology : AMB · 2025Article
- A framework for privacy-preserving similarity search of massive multi-party genomic data.Frontiers in plant science · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome.Microbiome · 2024Article
- GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs.Nucleic acids research · 2024Article
- Article
- Combining DNA and protein alignments to improve genome annotation with LiftOn.bioRxiv : the preprint server for biology · 2024Article
- Article
- RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures.Bioinformatics (Oxford, England) · 2023Article
- DandD: efficient measurement of sequence growth and similarity.bioRxiv : the preprint server for biology · 2023Article
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2 authors.
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Abstract
A genomic sketch is a small, probabilistic representation of the set of k-mers in a sequencing data set. Sketches are building blocks for large-scale analyses that consider similarities between many pairs of sequences or sequence collections. Although existing tools can easily compare tens of thousands of genomes, data sets can reach millions of sequences and beyond. Popular tools also fail to consider k-mer multiplicities, making them less applicable in quantitative settings. Here, we describe a method called Dashing 2 that builds on the SetSketch data structure. SetSketch is related to HyperLogLog (HLL) but discards use of leading zero count in favor of a truncated logarithm of adjustable base. Unlike HLL, SetSketch can perform multiplicity-aware sketching when combined with the ProbMinHash method. Dashing 2 integrates locality-sensitive hashing to scale all-pairs comparisons to millions of sequences. It achieves superior similarity estimates for the Jaccard coefficient and average nucleotide identity compared with the original Dashing, but in much less time while using the same-sized sketch. Dashing 2 is a free, open source software.
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