ArticleBioinformatics (Oxford, England)2023
Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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43 citing papers in PubMed.
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- Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures.bioRxiv : the preprint server for biology · 2026Article
- An improved Solanum verrucosum genome provides insight into potato centromeres and epigenetic regulation.G3 (Bethesda, Md.) · 2026Article
- Hash functions in nucleotide sequence analysis.Genome research · 2026Review
- Long-read assembly reveals vast transcriptional complexity in the placenta associated with metabolic and endocrine function.Nature communications · 2026Article
- Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes.bioRxiv : the preprint server for biology · 2026Article
- Improving isoform-level eQTL and integrative genetic analyses of breast cancer risk with long-read RNA transcript assemblies.bioRxiv : the preprint server for biology · 2026Article
- krepp: a k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement.Genome biology · 2026Article
- Benchmarking of Oxford Nanopore whole genome sequencing for germline variant and CpG methylation detection across Canada's national platform for genome sequencing and analysis.Frontiers in genetics · 2026Article
- Puzzler: scalable one-command platinum-quality genome assembly from HiFi and Hi-C.Bioinformatics advances · 2026Article
- Origin and evolution of acrocentric chromosomes in human and great apes.bioRxiv : the preprint server for biology · 2025Article
- SAFARI: pangenome alignment of ancient DNA using purine/pyrimidine encodings.NAR genomics and bioinformatics · 2025Article
- Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding.Nature communications · 2025Article
- Seqwin: Ultrafast identification of signature sequences in microbial genomes.bioRxiv : the preprint server for biology · 2025Article
- Complete genome assemblies of two mouse subspecies reveal structural diversity of telomeres and centromeres.Nature genetics · 2025Article
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Abstract
motivationThe Jaccard similarity on k-mer sets has shown to be a convenient proxy for sequence identity. By avoiding expensive base-level alignments and comparing reduced sequence representations, tools such as MashMap can scale to massive numbers of pairwise comparisons while still providing useful similarity estimates. However, due to their reliance on minimizer winnowing, previous versions of MashMap were shown to be biased and inconsistent estimators of Jaccard similarity. This directly impacts downstream tools that rely on the accuracy of these estimates.
resultsTo address this, we propose the minmer winnowing scheme, which generalizes the minimizer scheme by use of a rolling minhash with multiple sampled k-mers per window. We show both theoretically and empirically that minmers yield an unbiased estimator of local Jaccard similarity, and we implement this scheme in an updated version of MashMap. The minmer-based implementation is over 10 times faster than the minimizer-based version under the default ANI threshold, making it well-suited for large-scale comparative genomics applications. AVAILABILITY AND IMPLEMENTATION: MashMap3 is available at https://github.com/marbl/MashMap.
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