ArticleBioinformatics (Oxford, England)2023
Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes.
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 30 papers, 1 of them a synthesis that pooled it.
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30 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Identification of transporter-dependent capsular loci associated with the invasive potential of Escherichia coli.Nature microbiology · 2026Article
- Optimizing sparse and skew hashing: fasterbioRxiv : the preprint server for biology · 2026Article
- Kaminari: a frugal colored index for approximateBioinformatics advances · 2026Article
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- Scaling laws of bacterial and archaeal plasmids.Nature communications · 2025Article
- Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment.Bioinformatics (Oxford, England) · 2025Article
- Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm.Genome research · 2025Article
- K2R: Tinted de Bruijn graphs implementation for efficient read extraction from sequencing datasets.Bioinformatics advances · 2025Article
- The backpack quotient filter: A dynamic and space-efficient data structure for queryingiScience · 2024Article
- Seamless, rapid, and accurate analyses of outbreak genomic data using splitGenome research · 2024Article
- Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn GraphsJournal of computational biology : a journal of computational molecular cell biology · 2024Article
- Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k-mer sets.Bioinformatics (Oxford, England) · 2024Article
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4 authors.
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Abstract
motivationHuge datasets containing whole-genome sequences of bacterial strains are now commonplace and represent a rich and important resource for modern genomic epidemiology and metagenomics. In order to efficiently make use of these datasets, efficient indexing data structures-that are both scalable and provide rapid query throughput-are paramount.
resultsHere, we present Themisto, a scalable colored k-mer index designed for large collections of microbial reference genomes, that works for both short and long read data. Themisto indexes 179 thousand Salmonella enterica genomes in 9 h. The resulting index takes 142 gigabytes. In comparison, the best competing tools Metagraph and Bifrost were only able to index 11 000 genomes in the same time. In pseudoalignment, these other tools were either an order of magnitude slower than Themisto, or used an order of magnitude more memory. Themisto also offers superior pseudoalignment quality, achieving a higher recall than previous methods on Nanopore read sets. AVAILABILITY AND IMPLEMENTATION: Themisto is available and documented as a C++ package at https://github.com/algbio/themisto available under the GPLv2 license.
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