ArticleNucleic acids research2024
Pasa: leveraging population pangenome graph to scaffold prokaryote genome assemblies.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- The telomere-to-telomere genome and comparative analysis from algae to higher plants reveal origin and evolution of biosynthesis of chlorogenic acid pathway and production in ramie (Horticulture research · 2026Article
- Leveraging microbial phylogeny for computational efficiency.Nature reviews. Microbiology · 2026Article
- Near telomere-to-telomere genome assembly of the stone loach (Traccatichthys pulcher).Scientific data · 2026Article
- Pangenome-guided sequence assembly via binary optimization.Briefings in bioinformatics · 2026Article
- Chromosome-level genome assembly for an edible protein microalgae Auxenochlorella pyrenoidosa.Scientific data · 2025Article
- Near telomere-to-telomere genome assembly of the blackspot tuskfish (Choerodon schoenleinii).Scientific data · 2025Article
- Article
- Efficient inference of large prokaryotic pangenomes with PanTA.Genome biology · 2024Article
- AMRomics: a scalable workflow to analyze large microbial genome collections.BMC genomics · 2024Article
- AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance.BMC bioinformatics · 2024Article
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Authors and funding
10 authors.
Funding
Abstract
Whole genome sequencing has increasingly become the essential method for studying the genetic mechanisms of antimicrobial resistance and for surveillance of drug-resistant bacterial pathogens. The majority of bacterial genomes sequenced to date have been sequenced with Illumina sequencing technology, owing to its high-throughput, excellent sequence accuracy, and low cost. However, because of the short-read nature of the technology, these assemblies are fragmented into large numbers of contigs, hindering the obtaining of full information of the genome. We develop Pasa, a graph-based algorithm that utilizes the pangenome graph and the assembly graph information to improve scaffolding quality. By leveraging the population information of the bacteria species, Pasa is able to utilize the linkage information of the gene families of the species to resolve the contig graph of the assembly. We show that our method outperforms the current state of the arts in terms of accuracy, and at the same time, is computationally efficient to be applied to a large number of existing draft assemblies.
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Registered trials
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