ArticleGenome biology2021
Pandora: nucleotide-resolution bacterial pan-genomics with reference 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 46 papers.
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Who cites it
46 citing papers in PubMed.
- Representation and detection of inversions in pangenome graphs.NAR genomics and bioinformatics · 2026Article
- ALPAR: automated learning pipeline for antimicrobial resistance.Bioinformatics (Oxford, England) · 2026Article
- Efficient sequence alignment against millions of prokaryotic genomes with LexicMap.Nature biotechnology · 2026Article
- PG2: algorithms and a web-based tool for effective layout and visual analysis of pangenome graphs.BMC bioinformatics · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Kente: A Graph-based Pangenomic Approach for Horizontal Gene Transfer Detection in Microbiomes.bioRxiv : the preprint server for biology · 2026Article
- Compressive pangenomics using mutation-annotated networks.Nature genetics · 2026Article
- Panalyze: automated virus pangenome variation graph construction, analysis and annotation.Bioinformatics advances · 2026Article
- A multi-isolate genomic approach identifies diverseMicrobial genomics · 2025Article
- Reference-Free Variant Calling with Local Graph Construction with ska lo (SKA).Molecular biology and evolution · 2025Article
- Integrated population clustering and genomic epidemiology with PopPIPE.Microbial genomics · 2025Article
- Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.mSystems · 2025Review
- Quantifying the Evolutionary Dynamics of Structure and Content in Closely Related E. coli Genomes.Molecular biology and evolution · 2025Article
- PangeBlocks: customized construction of pangenome graphs via maximal blocks.BMC bioinformatics · 2024Article
- Seamless, rapid, and accurate analyses of outbreak genomic data using splitGenome research · 2024Article
- When less is more: sketching with minimizers in genomics.Genome biology · 2024Review
- Article
- Review
- CELEBRIMBOR: core and accessory genes from metagenomes.Bioinformatics (Oxford, England) · 2024Article
- Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs.Genome research · 2024Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
We present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the accessory genome, methods which analyze SNPs in just the core genome have unsatisfactory limitations. Pandora approximates a sequenced genome as a recombinant of references, detects novel variation and pan-genotypes multiple samples. Using a reference graph of 578 Escherichia coli genomes, we compare 20 diverse isolates. Pandora recovers more rare SNPs than single-reference-based tools, is significantly better than picking the closest RefSeq reference, and provides a stable framework for analyzing diverse samples without reference bias.
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