ArticleBioinformatics (Oxford, England)2022
The minimizer Jaccard estimator is biased and inconsistent.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
- A k-mer-based estimator of the substitution rate between repetitive sequences.Algorithms for molecular biology : AMB · 2026Article
- The gift of novelty: repeat-robust k-mer-based estimators of mutation rates.Bioinformatics (Oxford, England) · 2026Article
- Seqwin: ultrafast identification of signature sequences in microbial genomes.Bioinformatics (Oxford, England) · 2026Article
- The gift of novelty: repeat-robustbioRxiv : the preprint server for biology · 2026Article
- High-resolution metagenome assembly for modern long reads with myloasm.Nature biotechnology · 2026Article
- chewBBACA 3: lowering the barrier for scalable and detailed whole- and core-genome multilocus sequence typing.Genome medicine · 2026Article
- Seqwin: Ultrafast identification of signature sequences in microbial genomes.bioRxiv : the preprint server for biology · 2025Article
- High-resolution metagenome assembly for modern long reads with myloasm.bioRxiv : the preprint server for biology · 2025Article
- KPop: accurate and scalable comparative analysis of microbial genomes by sequence embeddings.Genome biology · 2025Article
- A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2025Article
- When less is more: sketching with minimizers in genomics.Genome biology · 2024Review
- ESKEMAP: exact sketch-based read mapping.Algorithms for molecular biology : AMB · 2024Article
- Creating and Using Minimizer Sketches in Computational Genomics.Journal of computational biology : a journal of computational molecular cell biology · 2023Review
- Skani enables accurate and efficient genome comparison for modern metagenomic datasets.Nature methods · 2023Article
- Fast and robust metagenomic sequence comparison through sparse chaining with skani.Nature methods · 2023Article
- Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation.Bioinformatics (Oxford, England) · 2023Article
- Exact Sketch-Based Read Mapping.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2023Article
- A survey of mapping algorithms in the long-reads era.Genome biology · 2023Review
- Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation.bioRxiv : the preprint server for biology · 2023Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationSketching is now widely used in bioinformatics to reduce data size and increase data processing speed. Sketching approaches entice with improved scalability but also carry the danger of decreased accuracy and added bias. In this article, we investigate the minimizer sketch and its use to estimate the Jaccard similarity between two sequences.
resultsWe show that the minimizer Jaccard estimator is biased and inconsistent, which means that the expected difference (i.e. the bias) between the estimator and the true value is not zero, even in the limit as the lengths of the sequences grow. We derive an analytical formula for the bias as a function of how the shared k-mers are laid out along the sequences. We show both theoretically and empirically that there are families of sequences where the bias can be substantial (e.g. the true Jaccard can be more than double the estimate). Finally, we demonstrate that this bias affects the accuracy of the widely used mashmap read mapping tool. AVAILABILITY AND IMPLEMENTATION: Scripts to reproduce our experiments are available at https://github.com/medvedevgroup/minimizer-jaccard-estimator/tree/main/reproduce. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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