ArticleGenome biology2023
Matchtigs: minimum plain text representation of k-mer sets.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Optimizing sparse and skew hashing: faster k-mer dictionaries.Bioinformatics (Oxford, England) · 2026Article
- Elucidating Transitions ofJournal of computational biology : a journal of computational molecular cell biology · 2026Article
- FroM Superstring to Indexing: a space-efficient index for unconstrainedBioinformatics advances · 2026Article
- Prokrustean Graph: A substring index for rapid k-mer size analysis.bioRxiv : the preprint server for biology · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time.Algorithms for molecular biology : AMB · 2023Article
- Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT.Genome research · 2023Article
- Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time.Research square · 2023Article
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5 authors.
Funding
Abstract
We propose a polynomial algorithm computing a minimum plain-text representation of k-mer sets, as well as an efficient near-minimum greedy heuristic. When compressing read sets of large model organisms or bacterial pangenomes, with only a minor runtime increase, we shrink the representation by up to 59% over unitigs and 26% over previous work. Additionally, the number of strings is decreased by up to 97% over unitigs and 90% over previous work. Finally, a small representation has advantages in downstream applications, as it speeds up SSHash-Lite queries by up to 4.26× over unitigs and 2.10× over previous work.
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Registered trials
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