ArticleBioinformatics (Oxford, England)2022
ODGI: understanding pangenome graphs.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers, 1 of them a synthesis that pooled it.
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Who cites it
115 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes.Genome biology and evolution · 2023Pooled it
- Insights into goatpox virus and sheeppox virus genomes from pangenome graphs.Archives of virology · 2026Article
- Resolving missing human polymorphic inversions and other complex variants from ultralong read data.Genome research · 2026Article
- Candidate genes with antagonistic roles in stomatal development are associated with population-wide variation in apple.Horticulture research · 2026Article
- COSIGT: population-scalable genotyping of complex loci from low-coverage sequencing data using pangenome graphs.Genome biology · 2026Article
- Four haplotype-resolved genome assemblies and a reference-free 66-haplotype pangenome graph for Cannabis sativa.Scientific data · 2026Article
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Telomere-to-telomere genome assembly and a pangenome for the rat.Cell genomics · 2026Article
- PangyPlot: multi-scale interactive visualization of pangenome variation graphs.Bioinformatics (Oxford, England) · 2026Article
- Bacterial DNA invasion triggers transposable element proliferation and genome expansion.bioRxiv : the preprint server for biology · 2026Article
- PG2: algorithms and a web-based tool for effective layout and visual analysis of pangenome graphs.BMC bioinformatics · 2026Article
- Navigating the pangenome coordinate system with Shredtools.bioRxiv : the preprint server for biology · 2026Article
- Haplotype graph analysis of PdR1 uncovers resistance diversity to Pierce's disease in Vitis arizonica and its hybrids.G3 (Bethesda, Md.) · 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
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures.bioRxiv : the preprint server for biology · 2026Article
- Article
- Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.Nature communications · 2026Article
- Pan-genome analysis uncovers extensive structural variations in Africa's indigenous legume crop cowpea.Nature communications · 2026Article
55 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
motivationPangenome graphs provide a complete representation of the mutual alignment of collections of genomes. These models offer the opportunity to study the entire genomic diversity of a population, including structurally complex regions. Nevertheless, analyzing hundreds of gigabase-scale genomes using pangenome graphs is difficult as it is not well-supported by existing tools. Hence, fast and versatile software is required to ask advanced questions to such data in an efficient way.
resultsWe wrote Optimized Dynamic Genome/Graph Implementation (ODGI), a novel suite of tools that implements scalable algorithms and has an efficient in-memory representation of DNA pangenome graphs in the form of variation graphs. ODGI supports pre-built graphs in the Graphical Fragment Assembly format. ODGI includes tools for detecting complex regions, extracting pangenomic loci, removing artifacts, exploratory analysis, manipulation, validation and visualization. Its fast parallel execution facilitates routine pangenomic tasks, as well as pipelines that can quickly answer complex biological questions of gigabase-scale pangenome graphs. AVAILABILITY AND IMPLEMENTATION: ODGI is published as free software under the MIT open source license. Source code can be downloaded from https://github.com/pangenome/odgi and documentation is available at https://odgi.readthedocs.io. ODGI can be installed via Bioconda https://bioconda.github.io/recipes/odgi/README.html or GNU Guix https://github.com/pangenome/odgi/blob/master/guix.scm. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
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.