ArticleNature computational science2024
Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA.
Article in Nature computational science, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- A k-mer-based estimator of the substitution rate between repetitive sequences.Algorithms for molecular biology : AMB · 2026Article
- META-DIFF: a k-mer-based pipeline that detects differentially abundant sequences in metagenomics whole genome sequencing.Scientific reports · 2026Article
- Kaminari: a frugal colored index for approximateBioinformatics advances · 2026Article
- Article
- wholeskim: Utilising Genome Skims for Taxonomically Annotating Ancient DNA Metagenomes.Molecular ecology resources · 2025Article
- Logan: Planetary-Scale Genome Assembly Surveys Life's Diversity.bioRxiv : the preprint server for biology · 2025Article
- MUSET: set of utilities for constructing abundance unitig matrices from sequencing data.Bioinformatics (Oxford, England) · 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
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Authors and funding
7 authors.
Funding
Abstract
Public sequencing databases contain vast amounts of biological information, yet they are largely underutilized as it is challenging to efficiently search them for any sequence(s) of interest. We present kmindex, an approach that can index thousands of metagenomes and perform sequence searches in a fraction of a second. The index construction is an order of magnitude faster than previous methods, while search times are two orders of magnitude faster. With negligible false positive rates below 0.01%, kmindex outperforms the precision of existing approaches by four orders of magnitude. Here we demonstrate the scalability of kmindex by successfully indexing 1,393 marine seawater metagenome samples from the Tara Oceans project. Additionally, we introduce the publicly accessible web server Ocean Read Atlas, which enables real-time queries on the Tara Oceans dataset.
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Registered trials
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