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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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac308","type":"journal-article","created":{"date-parts":[[2022,5,10]],"date-time":"2022-05-10T07:23:03Z","timestamp":1652167383000},"page":"3319-3326","source":"Crossref","is-referenced-by-count":204,"title":["ODGI: understanding pangenome graphs"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9744-131X","authenticated-orcid":false,"given":"Andrea","family":"Guarracino","sequence":"first","affiliation":[{"name":"Genomics Research Centre, Human Technopole , Milan 20157, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3326-817X","authenticated-orcid":false,"given":"Simon","family":"Heumos","sequence":"additional","affiliation":[{"name":"Quantitative Biology Center (QBiC), University of T\u00fcbingen , T\u00fcbingen 72076, Germany"},{"name":"Biomedical Data Science, Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen 72076, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4375-0691","authenticated-orcid":false,"given":"Sven","family":"Nahnsen","sequence":"additional","affiliation":[{"name":"Quantitative Biology Center (QBiC), University of T\u00fcbingen , T\u00fcbingen 72076, Germany"},{"name":"Biomedical Data Science, Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen 72076, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pjotr","family":"Prins","sequence":"additional","affiliation":[{"name":"Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center , Memphis, TN 38163, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3821-631X","authenticated-orcid":false,"given":"Erik","family":"Garrison","sequence":"additional","affiliation":[{"name":"Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center , Memphis, TN 38163, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,5,13]]},"reference":[{"key":"2023041407595212700_","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1038\/s41586-020-2871-y","article-title":"Progressive cactus is a multiple-genome aligner for the thousand-genome era","volume":"587","author":"Armstrong","year":"2020","journal-title":"Nature"},{"key":"2023041407595212700_","doi-asserted-by":"crossref","first-page":"5086","DOI":"10.1093\/bioinformatics\/btz443","article-title":"Full-length de novo viral quasispecies assembly through variation graph construction","volume":"35","author":"Baaijens","year":"2019","journal-title":"Bioinformatics"},{"key":"2023041407595212700_","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1186\/s13059-019-1774-4","article-title":"Is it time to change the reference genome?","volume":"20","author":"Ballouz","year":"2019","journal-title":"Genome Biol"},{"key":"2023041407595212700_","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1038\/s41477-020-0733-0","article-title":"Plant pan-genomes are the new reference","volume":"6","author":"Bayer","year":"2020","journal-title":"Nat. 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