ArticleNature communications2020
Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Article
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- Genomic and Ecological Flexibility Shape the Global Distribution of a Black Fungus.Environmental microbiology · 2026Article
- ntSynt: multi-genome synteny detection using minimizer graph mappings.BMC biology · 2025Article
- Quantifying Hierarchical Conflicts in Homology Statements.Journal of molecular evolution · 2025Article
- Insights into Yersinia pestis evolution through rearrangement analysis of 242 complete genomes.Nature genetics · 2025Article
- Review
- MAFin: motif detection in multiple alignment files.Bioinformatics (Oxford, England) · 2025Article
- Conservation assessment of human splice site annotation based on a 470-genome alignment.Nucleic acids research · 2025Article
- Conservation assessment of human splice site annotation based on a 470-genome alignment.bioRxiv : the preprint server for biology · 2025Article
- The hidden bacterial microproteome.Molecular cell · 2025Article
- PRDM9 drives the location and rapid evolution of recombination hotspots in salmonid fish.PLoS biology · 2025Article
- Complexity welcome: Pangenome graphs for comprehensive population genomics.Quantitative plant biology · 2025Review
- Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn GraphsJournal of computational biology : a journal of computational molecular cell biology · 2024Article
- Five centuries of consanguinity, isolation, health, and conflict in Las Gobas: A Northern Medieval Iberian necropolis.Science advances · 2024Article
- The promise and pitfalls of synteny in phylogenomics.PLoS biology · 2024Article
- Chromosome-Level Assembly and Annotation of the Pearly Heath Coenonympha arcania Butterfly Genome.Genome biology and evolution · 2024Article
- The Cryptic Bacterial Microproteome.bioRxiv : the preprint server for biology · 2024Article
- CoreDetector: a flexible and efficient program for core-genome alignment of evolutionary diverse genomes.Bioinformatics (Oxford, England) · 2023Article
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2 authors.
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Abstract
Multiple whole-genome alignment is a challenging problem in bioinformatics. Despite many successes, current methods are not able to keep up with the growing number, length, and complexity of assembled genomes, especially when computational resources are limited. Approaches based on compacted de Bruijn graphs to identify and extend anchors into locally collinear blocks have potential for scalability, but current methods do not scale to mammalian genomes. We present an algorithm, SibeliaZ-LCB, for identifying collinear blocks in closely related genomes based on analysis of the de Bruijn graph. We further incorporate this into a multiple whole-genome alignment pipeline called SibeliaZ. SibeliaZ shows run-time improvements over other methods while maintaining accuracy. On sixteen recently-assembled strains of mice, SibeliaZ runs in under 16 hours on a single machine, while other tools did not run to completion for eight mice within a week. SibeliaZ makes a significant step towards improving scalability of multiple whole-genome alignment and collinear block reconstruction algorithms on a single machine.
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