ArticleBioinformatics (Oxford, England)2014
SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- deMEM: a novel divide-and-conquer framework based on de Bruijn graph for scalable multiple sequence alignment.GigaScience · 2026Article
- Developing pangenomes for large and complex plant genomes and their representation formats.Journal of advanced research · 2025Review
- Review
- A survey of sequence-to-graph mapping algorithms in the pangenome era.Genome biology · 2025Review
- From map to blueprint: the plant pan-genome unraveling genetic mysteries and powering precision breeding.Frontiers in plant science · 2025Review
- Panacus: fast and exact pangenome growth and core size estimation.Bioinformatics (Oxford, England) · 2024Article
- When less is more: sketching with minimizers in genomics.Genome biology · 2024Review
- 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
- Panacus: fast and exact pangenome growth and core size estimation.bioRxiv : the preprint server for biology · 2024Article
- Methods for Pangenomic Core Detection.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Pan-genome de Bruijn graph using the bidirectional FM-index.BMC bioinformatics · 2023Article
- On weighted k-mer dictionaries.Algorithms for molecular biology : AMB · 2023Article
- PRAWNS: compact pan-genomic features for whole-genome population genomics.Bioinformatics (Oxford, England) · 2023Article
- Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2.Genome biology · 2022Article
- Sequence-based pangenomic core detection.iScience · 2022Article
- Review
- Review
- Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species.International journal of molecular sciences · 2022Review
- Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections.Bioinformatics (Oxford, England) · 2021Article
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Authors and funding
3 authors.
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Abstract
motivationGenomics is expanding from a single reference per species paradigm into a more comprehensive pan-genome approach that analyzes multiple individuals together. A compressed de Bruijn graph is a sophisticated data structure for representing the genomes of entire populations. It robustly encodes shared segments, simple single-nucleotide polymorphisms and complex structural variations far beyond what can be represented in a collection of linear sequences alone.
resultsWe explore deep topological relationships between suffix trees and compressed de Bruijn graphs and introduce an algorithm, splitMEM, that directly constructs the compressed de Bruijn graph in time and space linear to the total number of genomes for a given maximum genome size. We introduce suffix skips to traverse several suffix links simultaneously and use them to efficiently decompose maximal exact matches into graph nodes. We demonstrate the utility of splitMEM by analyzing the nine-strain pan-genome of Bacillus anthracis and up to 62 strains of Escherichia coli, revealing their core-genome properties.
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Registered trials
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.