{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T01:20:39Z","timestamp":1775265639397,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2024,11,29]],"date-time":"2024-11-29T00:00:00Z","timestamp":1732838400000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1U01HG010973"],"award-info":[{"award-number":["1U01HG010973"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Using 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).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We 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 &amp;lt;1 h.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae720","type":"journal-article","created":{"date-parts":[[2024,11,27]],"date-time":"2024-11-27T15:27:45Z","timestamp":1732721265000},"source":"Crossref","is-referenced-by-count":26,"title":["Panacus: fast and exact pangenome growth and core size estimation"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2139-3259","authenticated-orcid":false,"given":"Luca","family":"Parmigiani","sequence":"first","affiliation":[{"name":"Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University , Bielefeld 33615,","place":["Germany"]}]},{"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,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4656-7155","authenticated-orcid":false,"given":"Jens","family":"Stoye","sequence":"additional","affiliation":[{"name":"Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University , Bielefeld 33615,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9376-1030","authenticated-orcid":false,"given":"Tobias","family":"Marschall","sequence":"additional","affiliation":[{"name":"Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf , D\u00fcsseldorf 40225,","place":["Germany"]},{"name":"Center for Digital Medicine, Heinrich Heine University D\u00fcsseldorf , D\u00fcsseldorf 40225,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3720-6227","authenticated-orcid":false,"given":"Daniel","family":"Doerr","sequence":"additional","affiliation":[{"name":"Center for Digital Medicine, Heinrich Heine University D\u00fcsseldorf , D\u00fcsseldorf 40225,","place":["Germany"]},{"name":"Department for Endocrinology and Diabetology, Medical Faculty and University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf , D\u00fcsseldorf 40225,","place":["Germany"]},{"name":"German Diabetes Center (DDZ), Leibniz Institute for Diabetes Research , D\u00fcsseldorf 40225,","place":["Germany"]}]}],"member":"286","published-online":{"date-parts":[[2024,11,29]]},"reference":[{"key":"2024122317384757000_btae720-B1","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1038\/nrmicro2123","article-title":"Sequencing the species pan-genome","volume":"7","author":"Bentley","year":"2009","journal-title":"Nat Rev 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