{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:09Z","timestamp":1772138049084,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2021,10,8]],"date-time":"2021-10-08T00:00:00Z","timestamp":1633651200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Development Regional Fund","award":["AC16\/00039"],"award-info":[{"award-number":["AC16\/00039"]}]},{"name":"European Development Regional Fund","award":["PI18\/01942"],"award-info":[{"award-number":["PI18\/01942"]}]},{"name":"European Development Regional Fund","award":["CB06\/02\/0053"],"award-info":[{"award-number":["CB06\/02\/0053"]}]},{"name":"Regional Government of Madrid","award":["CAM-B2017\/BMD-3691"],"award-info":[{"award-number":["CAM-B2017\/BMD-3691"]}]},{"name":"Sara Borrell","award":["CD17\/00272"],"award-info":[{"award-number":["CD17\/00272"]}]},{"name":"pFIS predoctoral fellowships","award":["FI19\/00366"],"award-info":[{"award-number":["FI19\/00366"]}]},{"name":"pFIS predoctoral fellowships","award":["FI19\/00182"],"award-info":[{"award-number":["FI19\/00182"]}]},{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>We present the Pangenome Analysis Toolkit (PATO) designed to simultaneously analyze thousands of genomes using a desktop computer. The tool performs common tasks of pangenome analysis such as core-genome definition and accessory genome properties and includes new features that help characterize population structure, annotate pathogenic features and create gene sharedness networks. PATO has been developed in R to integrate with the large set of tools available for genetic, phylogenetic and statistical analysis in this environment.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>PATO can perform the most demanding bioinformatic analyses in minutes with an accuracy comparable to state-of-the-art software but 20\u201330\u00d7 times faster. PATO also integrates all the necessary functions for the complete analysis of the most common objectives in microbiology studies. Finally, PATO includes the necessary tools for visualizing the results and can be integrated with other analytical packages available in R.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availabilityand implementation<\/jats:title>\n                    <jats:p>The source code for PATO is freely available at https:\/\/github.com\/irycisBioinfo\/PATO under the GPLv3 license.<\/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\/btab697","type":"journal-article","created":{"date-parts":[[2021,10,7]],"date-time":"2021-10-07T08:49:37Z","timestamp":1633596577000},"page":"4564-4566","source":"Crossref","is-referenced-by-count":23,"title":["PATO: Pangenome Analysis Toolkit"],"prefix":"10.1093","volume":"37","author":[{"given":"Miguel D","family":"Fern\u00e1ndez-de-Bobadilla","sequence":"first","affiliation":[{"name":"Department of Microbiology, University Hospital Ram\u00f3n y Cajal, IRYCIS , Madrid, Spain"},{"name":"Bioinformatics Unit, University Hospital Ram\u00f3n y Cajal, IRYCIS , Madrid, Spain"}]},{"given":"Alba","family":"Talavera-Rodr\u00edguez","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, University Hospital Ram\u00f3n y Cajal, IRYCIS , Madrid, Spain"},{"name":"Department of Infectious Diseases, University Hospital Ramon y Cajal, IRYCIS , Madrid, Spain"}]},{"given":"Luc\u00eda","family":"Chac\u00f3n","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, University Hospital Ram\u00f3n y Cajal, IRYCIS , Madrid, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7930-3033","authenticated-orcid":false,"given":"Fernando","family":"Baquero","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University Hospital Ram\u00f3n y Cajal, IRYCIS , Madrid, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8228-3491","authenticated-orcid":false,"given":"Teresa M","family":"Coque","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University Hospital Ram\u00f3n y Cajal, IRYCIS , Madrid, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0870-9500","authenticated-orcid":false,"given":"Val F","family":"Lanza","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University Hospital Ram\u00f3n y Cajal, IRYCIS , Madrid, Spain"},{"name":"Bioinformatics Unit, University Hospital Ram\u00f3n y Cajal, IRYCIS , Madrid, Spain"}]}],"member":"286","published-online":{"date-parts":[[2021,10,8]]},"reference":[{"key":"2023061310545366200_btab697-B1","doi-asserted-by":"crossref","first-page":"e000224","DOI":"10.1099\/mgen.0.000224","article-title":"mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species","volume":"4","author":"Arredondo-Alonso","year":"2018","journal-title":"Microb. Genomics"},{"key":"2023061310545366200_btab697-B2","first-page":"361","author":"Bastian","year":"2009"},{"key":"2023061310545366200_btab697-B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/giz119","article-title":"PIRATE: a fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria","volume":"8","author":"Bayliss","year":"2019","journal-title":"Gigascience"},{"key":"2023061310545366200_btab697-B4","doi-asserted-by":"crossref","DOI":"10.1038\/nbt.4314","article-title":"Dimensionality reduction for visualizing single-cell data using UMAP","author":"Becht","year":"2019","journal-title":"Nat. Biotechnol"},{"key":"2023061310545366200_btab697-B5","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother"},{"key":"2023061310545366200_btab697-B6","doi-asserted-by":"crossref","first-page":"D694","DOI":"10.1093\/nar\/gkv1239","article-title":"VFDB 2016: hierarchical and refined dataset for big data analysis-10 years on","volume":"44","author":"Chen","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023061310545366200_btab697-B7","doi-asserted-by":"crossref","first-page":"e5","DOI":"10.1093\/nar\/gkx977","article-title":"panX: pan-genome analysis and exploration","volume":"46","author":"Ding","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023061310545366200_btab697-B8","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1007\/978-1-4939-9877-7_24","article-title":"Statistical analysis of accessory genome","volume":"2075","author":"Fern\u00e1ndez-de-Bobadilla","year":"2020","journal-title":"Methods Mol. Biol"},{"key":"2023061310545366200_btab697-B9","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1093\/bioinformatics\/btw601","article-title":"AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks","volume":"33","author":"Lanza","year":"2017","journal-title":"Bioinformatics"},{"key":"2023061310545366200_btab697-B10","article-title":"Minimap2: pairwise alignment for nucleotide sequences","author":"Li","year":"2018","journal-title":"Bioinformatics, 34, 3094-3100"},{"key":"2023061310545366200_btab697-B11","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: fast genome and metagenome distance estimation using MinHash","volume":"17","author":"Ondov","year":"2016","journal-title":"Genome Biol"},{"key":"2023061310545366200_btab697-B12","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"2023061310545366200_btab697-B13","first-page":"lqaa106","article-title":"PanACoTA: a modular tool for massive microbial comparative genomics","volume":"3","author":"Perrin","year":"2021","journal-title":"NAR Genomics Bioinf"},{"key":"2023061310545366200_btab697-B14","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi1112s47","article-title":"BEDTools: the Swiss-Army tool for genome feature analysis","author":"Quinlan","year":"2014","journal-title":"Curr. Protoc. Bioinf"},{"key":"2023061310545366200_btab697-B15","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"2023061310545366200_btab697-B16","doi-asserted-by":"crossref","first-page":"2542","DOI":"10.1038\/s41467-018-04964-5","article-title":"Clustering huge protein sequence sets in linear time","volume":"9","author":"Steinegger","year":"2018","journal-title":"Nat. Commun"},{"key":"2023061310545366200_btab697-B17","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1186\/s13059-020-02090-4","article-title":"Producing polished prokaryotic pangenomes with the Panaroo pipeline","volume":"21","author":"Tonkin-Hill","year":"2020","journal-title":"Genome Biol"},{"key":"2023061310545366200_btab697-B18","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1007\/978-3-030-38281-0_4","volume-title":"The Pangenome: Diversity, Dynamics and Evolution of Genomes","author":"Vernikos","year":"2020"},{"key":"2023061310545366200_btab697-B19","doi-asserted-by":"crossref","first-page":"1667","DOI":"10.1101\/gr.260828.120","article-title":"Accurate reconstruction of bacterial pan- And core genomes with PEPPAN","volume":"30","author":"Zhou","year":"2020","journal-title":"Genome Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab697\/40807421\/btab697.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/23\/4564\/50579711\/btab697.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/23\/4564\/50579711\/btab697.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,13]],"date-time":"2023-06-13T06:56:16Z","timestamp":1686639376000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/23\/4564\/6384566"}},"subtitle":[],"editor":[{"given":"Pier","family":"Luigi Martelli","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,10,8]]},"references-count":19,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2021,12,7]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab697","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.01.30.428878","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,12,1]]},"published":{"date-parts":[[2021,10,8]]}}}