{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T05:34:34Z","timestamp":1773466474666,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2021,10,3]],"date-time":"2021-10-03T00:00:00Z","timestamp":1633219200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Agropolis Fondation\u2019s \u2018GenomeHarvest\u2019 project","award":["ID 1504-006"],"award-info":[{"award-number":["ID 1504-006"]}]},{"name":"CIFRE doctoral","award":["2018\/1475"],"award-info":[{"award-number":["2018\/1475"]}]},{"name":"CGIAR Research Program"}],"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>Pangenomics evolved since its first applications on bacteria, extending from the study of genes for a given population to the study of all of its sequences available. While multiple methods are being developed to construct pangenomes in eukaryotic species there is still a gap for efficient and user-friendly visualization tools. Emerging graph representations come with their own challenges, and linearity remains a suitable option for user-friendliness.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce Panache, a tool for the visualization and exploration of linear representations of gene-based and sequence-based pangenomes. It uses a layout similar to genome browsers to display presence absence variations and additional tracks along a linear axis with a pangenomics perspective.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Panache is available at github.com\/SouthGreenPlatform\/panache under the MIT License.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab688","type":"journal-article","created":{"date-parts":[[2021,9,30]],"date-time":"2021-09-30T16:54:33Z","timestamp":1633020873000},"page":"4556-4558","source":"Crossref","is-referenced-by-count":25,"title":["Panache: a web browser-based viewer for linearized pangenomes"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2734-4327","authenticated-orcid":false,"given":"\u00c9loi","family":"Durant","sequence":"first","affiliation":[{"name":"DIADE, Univ Montpellier, CIRAD, IRD , Montpellier 34830, France"},{"name":"Syngenta Seeds SAS , Saint-Sauveur 31790, France"},{"name":"Bioversity International, Parc Scientifique Agropolis II , Montpellier 34397, France"},{"name":"French Institute of Bioinformatics (IFB)\u2014South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD , Montpellier 34398, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8522-7583","authenticated-orcid":false,"given":"Fran\u00e7ois","family":"Sabot","sequence":"additional","affiliation":[{"name":"DIADE, Univ Montpellier, CIRAD, IRD , Montpellier 34830, France"},{"name":"French Institute of Bioinformatics (IFB)\u2014South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD , Montpellier 34398, France"}]},{"given":"Matthieu","family":"Conte","sequence":"additional","affiliation":[{"name":"Syngenta Seeds SAS , Saint-Sauveur 31790, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0284-1885","authenticated-orcid":false,"given":"Mathieu","family":"Rouard","sequence":"additional","affiliation":[{"name":"Bioversity International, Parc Scientifique Agropolis II , Montpellier 34397, France"},{"name":"French Institute of Bioinformatics (IFB)\u2014South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD , Montpellier 34398, France"}]}],"member":"286","published-online":{"date-parts":[[2021,10,2]]},"reference":[{"key":"2023061310540763800_btab688-B1","doi-asserted-by":"crossref","first-page":"5318","DOI":"10.1093\/bioinformatics\/btz597","article-title":"Sequence tube maps: making graph genomes intuitive to commuters","volume":"35","author":"Beyer","year":"2019","journal-title":"Bioinformatics"},{"key":"2023061310540763800_btab688-B2","first-page":"118","article-title":"Computational pan-genomics: status, promises and challenges","volume":"19","year":"2018","journal-title":"Brief. 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