ArticleGenome biology2021
Simplitigs as an efficient and scalable representation of de Bruijn graphs.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 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
- 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
- Efficient and robust search of microbial genomes via phylogenetic compression.Nature methods · 2025Article
- Fractional hitting sets for efficient multiset sketching.Algorithms for molecular biology : AMB · 2025Article
- Bioinformatic Methodologies in Assessing Gut Microbiota.Microbiology research · 2024Article
- Compression algorithm for colored de Bruijn graphs.Algorithms for molecular biology : AMB · 2024Article
- Space-efficient computation of k-mer dictionaries for large values of k.Algorithms for molecular biology : AMB · 2024Article
- Compression Algorithm for Colored de Bruijn Graphs.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2023Article
- Accurate and fast graph-based pangenome annotation and clustering with ggCaller.Genome research · 2023Article
- 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
- Locality-preserving minimal perfect hashing of k-mers.Bioinformatics (Oxford, England) · 2023Article
- Matchtigs: minimum plain text representation of k-mer sets.Genome biology · 2023Article
- Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time.Research square · 2023Article
- The K-mer File Format: a standardized and compact disk representation of sets of k-mers.Bioinformatics (Oxford, England) · 2022Article
- Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2.Genome biology · 2022Article
- Sparse and skew hashing of K-mers.Bioinformatics (Oxford, England) · 2022Article
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Authors and funding
3 authors.
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Abstract
de Bruijn graphs play an essential role in bioinformatics, yet they lack a universal scalable representation. Here, we introduce simplitigs as a compact, efficient, and scalable representation, and ProphAsm, a fast algorithm for their computation. For the example of assemblies of model organisms and two bacterial pan-genomes, we compare simplitigs to unitigs, the best existing representation, and demonstrate that simplitigs provide a substantial improvement in the cumulative sequence length and their number. When combined with the commonly used Burrows-Wheeler Transform index, simplitigs reduce memory, and index loading and query times, as demonstrated with large-scale examples of GenBank bacterial pan-genomes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.