{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T12:39:52Z","timestamp":1773837592786,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2017,4,7]],"date-time":"2017-04-07T00:00:00Z","timestamp":1491523200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61272250"],"award-info":[{"award-number":["61272250"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61472246"],"award-info":[{"award-number":["61472246"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["J1210047"],"award-info":[{"award-number":["J1210047"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Pan-genome analyses are routinely carried out for bacteria to interpret the within-species gene presence\/absence variations (PAVs). However, pan-genome analyses are rare for eukaryotes due to the large sizes and higher complexities of their genomes. Here we proposed EUPAN, a eukaryotic pan-genome analysis toolkit, enabling automatic large-scale eukaryotic pan-genome analyses and detection of gene PAVs at a relatively low sequencing depth. In the previous studies, we demonstrated the effectiveness and high accuracy of EUPAN in the pan-genome analysis of 453 rice genomes, in which we also revealed widespread gene PAVs among individual rice genomes. Moreover, EUPAN can be directly applied to the current re-sequencing projects primarily focusing on single nucleotide polymorphisms.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>EUPAN is implemented in Perl, R and C\u2009++. It is supported under Linux and preferred for a computer cluster with LSF and SLURM job scheduling system. EUPAN together with its standard operating procedure (SOP) is freely available for non-commercial use (CC BY-NC 4.0) at http:\/\/cgm.sjtu.edu.cn\/eupan\/index.html.<\/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\/btx170","type":"journal-article","created":{"date-parts":[[2017,3,28]],"date-time":"2017-03-28T08:55:18Z","timestamp":1490691318000},"page":"2408-2409","source":"Crossref","is-referenced-by-count":59,"title":["EUPAN enables pan-genome studies of a large number of eukaryotic genomes"],"prefix":"10.1093","volume":"33","author":[{"given":"Zhiqiang","family":"Hu","sequence":"first","affiliation":[{"name":"Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China"},{"name":"Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai, China"}]},{"given":"Chen","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China"},{"name":"Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai, China"}]},{"given":"Kuang-chen","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China"}]},{"given":"Xixia","family":"Chu","sequence":"additional","affiliation":[{"name":"Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China"}]},{"given":"Yue","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China"}]},{"given":"Jinyuan","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China"},{"name":"Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai, China"}]},{"given":"Jianxin","family":"Shi","sequence":"additional","affiliation":[{"name":"Department of Genetic and Developmental Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China"}]},{"given":"Chaochun","family":"Wei","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China"},{"name":"Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai, China"}]}],"member":"286","published-online":{"date-parts":[[2017,4,7]]},"reference":[{"key":"2023063012505671600_btx170-B1","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2023063012505671600_btx170-B2","doi-asserted-by":"crossref","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"2023063012505671600_btx170-B3","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"2023063012505671600_btx170-B4","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1105\/tpc.113.119982","article-title":"Insights into the maize pan-genome and pan-transcriptome","volume":"26","author":"Hirsch","year":"2014","journal-title":"Plant Cell"},{"key":"2023063012505671600_btx170-B5","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. 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