ArticleFrontiers in genetics2023
Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of
Article in Frontiers in genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 17 citations in OpenAlex.
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- A novel Vector-Symbolic Architecture for graph encoding and its application to viral pangenome-based species classification.BioData mining · 2026Article
- Benchmarking within-sample minority variant detection with short-read sequencing inbioRxiv : the preprint server for biology · 2026Article
- The pangenome: a statistical model, not a fixed biological property.Bioinformatics advances · 2026Review
- Acute Respiratory Infections (ARIs): Current Etiological Perspectives and Advances in Viral Metagenomics-A Review.Viruses · 2025Review
- Ecology, global diversity and evolutionary mechanisms in the Mycobacterium tuberculosis complex.Nature reviews. Microbiology · 2025Review
- Gene conversion and duplication contribute to genetic variation in an outbreak ofMicrobial genomics · 2025Article
- The evolutionary history of the common bean (Phaseolus vulgaris) revealed by chloroplast and nuclear genomes analysis.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Toward a standardized framework for pangenome graph evaluation: assessing crop plant pangenome variation graph construction from multiple assemblies.GigaScience · 2025Article
- Current methods in the diagnosis of invasive meningococcal disease.Frontiers in pediatrics · 2025Review
- Pangenome graphs and their applications in biodiversity genomics.Nature genetics · 2025Review
- Cluster-efficient pangenome graph construction with nf-core/pangenome.Bioinformatics (Oxford, England) · 2024Article
- Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew.PLoS genetics · 2024Article
Corrections and comments
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Authors and funding
10 authors at 6 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies are conducted on highly variable bacterial genomes of the same species. Pangenome graphs provide an efficient model for representing and analyzing multiple genomes and their variants as a graph structure that includes all types of variations. In this study, we present a practical bioinformatics pipeline that employs the PanGenome Graph Builder and the Variation Graph toolkit to build pangenomes from assembled genomes, align whole genome sequencing data and call variants against a graph reference. The pangenome graph enables the identification of structural variants, rearrangements, and small variants (e.g., single nucleotide polymorphisms and insertions/deletions) simultaneously. We demonstrate that using a pangenome graph, instead of a single linear reference genome, improves mapping rates and variant calling for both simulated and real datasets of the pathogen
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