ArticleAlgorithms for molecular biology : AMB2023
Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time.
Article in Algorithms for molecular biology : AMB, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Optimizing sparse and skew hashing: faster k-mer dictionaries.Bioinformatics (Oxford, England) · 2026Article
- Optimizing sparse and skew hashing: fasterbioRxiv : the preprint server for biology · 2026Article
- Identification of genome size and heterozygosity in 510 Jujube (Frontiers in plant science · 2026Article
- FroM Superstring to Indexing: a space-efficient index for unconstrainedBioinformatics advances · 2026Article
- Swiftly identifying strongly unique k-mers.Algorithms for molecular biology : AMB · 2025Article
- Space-efficient computation of k-mer dictionaries for large values of k.Algorithms for molecular biology : AMB · 2024Article
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Authors and funding
2 authors.
Funding
Abstract
A fundamental operation in computational genomics is to reduce the input sequences to their constituent k-mers. For maximum performance of downstream applications it is important to store the k-mers in small space, while keeping the representation easy and efficient to use (i.e. without k-mer repetitions and in plain text). Recently, heuristics were presented to compute a near-minimum such representation. We present an algorithm to compute a minimum representation in optimal (linear) time and use it to evaluate the existing heuristics. Our algorithm first constructs the de Bruijn graph in linear time and then uses a Eulerian-cycle-based algorithm to compute the minimum representation, in time linear in the size of the output.
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