ArticleBioinformatics (Oxford, England)2024
Panacus: fast and exact pangenome growth and core size estimation.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Chromosome-level phylogenomics and genome evolution of the grape family.Nature plants · 2026Article
- Insights into goatpox virus and sheeppox virus genomes from pangenome graphs.Archives of virology · 2026Article
- Four haplotype-resolved genome assemblies and a reference-free 66-haplotype pangenome graph for Cannabis sativa.Scientific data · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Phylogeny-driven pangenome analysis uncovers the genomic landscape of domesticated and wild Armeniaca species.Horticulture research · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Graph-based pan-genome reveals structural and functional diversity across oil palm domestication gradients.BMC plant biology · 2026Article
- Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome.The New phytologist · 2026Article
- Article
- Evolutionary and methodological considerations when interpreting gene presence-absence variation in pangenomes.NAR genomics and bioinformatics · 2026Review
- Panalyze: automated virus pangenome variation graph construction, analysis and annotation.Bioinformatics advances · 2026Article
- A Pan-TE Map Reveals the Important Role of Transposable Elements in Gene Expression and Phenotypic Diversity in 2,311 Rapeseed Accessions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers.BMC bioinformatics · 2025Article
- Multispecies pangenomes reveal a pervasive influence of population size on structural variation.Science (New York, N.Y.) · 2025Article
- Pangenomics and single-cell transcriptomics uncover the genetic basis of continuous bearing trait in grapevine.Horticulture research · 2025Article
- Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding.Nature communications · 2025Article
- Reference-free identification and pangenome analysis of accessory chromosomes in a major fungal plant pathogen.NAR genomics and bioinformatics · 2025Article
- Oryza genome evolution through a tetraploid lens.Nature genetics · 2025Article
- Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants.bioRxiv : the preprint server for biology · 2025Article
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Abstract
motivationUsing a single linear reference genome poses a limitation to exploring the full genomic diversity of a species. The release of a draft human pangenome underscores the increasing relevance of pangenomics to overcome these limitations. Pangenomes are commonly represented as graphs, which can represent billions of base pairs of sequence. Presently, there is a lack of scalable software able to perform key tasks on pangenomes, such as quantifying universally shared sequence across genomes (the core genome) and measuring the extent of genomic variability as a function of sample size (pangenome growth).
resultsWe introduce Panacus (pangenome-abacus), a tool designed to rapidly perform these tasks and visualize the results in interactive plots. Panacus can process GFA files, the accepted standard for pangenome graphs, and is able to analyze a human pangenome graph with 110 million nodes in <1 h. AVAILABILITY AND IMPLEMENTATION: Panacus is implemented in Rust and is published as Open Source software under the MIT license. The source code and documentation are available at https://github.com/marschall-lab/panacus. Panacus can be installed via Bioconda at https://bioconda.github.io/recipes/panacus/README.html.
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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.