{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T17:09:26Z","timestamp":1793207366200,"version":"4.5.0"},"reference-count":47,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2024,6,12]],"date-time":"2024-06-12T00:00:00Z","timestamp":1718150400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,6,12]],"date-time":"2024-06-12T00:00:00Z","timestamp":1718150400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["iMeta"],"published-print":{"date-parts":[[2024,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The life cycle of genome builds spans interlocking pillars of assembly, annotation, and comparative genomics to drive biological insights. While tools exist to address each pillar separately, there is a growing need for tools to integrate different pillars of a genome project holistically. For example, comparative approaches can provide quality control of assembly or annotation; genome assembly, in turn, can help to identify artifacts that may complicate the interpretation of genome comparisons. The JCVI library is a versatile Python\u2010based library that offers a suite of tools that excel across these pillars. Featuring a modular design, the JCVI library provides high\u2010level utilities for tasks such as format parsing, graphics generation, and manipulation of genome assemblies and annotations. Supporting genomics algorithms like MCscan and ALLMAPS are widely employed in building genome releases, producing publication\u2010ready figures for quality assessment and evolutionary inference. Developed and maintained collaboratively, the JCVI library emphasizes quality and reusability.<\/jats:p>","DOI":"10.1002\/imt2.211","type":"journal-article","created":{"date-parts":[[2024,6,13]],"date-time":"2024-06-13T02:14:03Z","timestamp":1718244843000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":529,"title":["JCVI: A versatile toolkit for comparative genomics analysis"],"prefix":"10.1002","volume":"3","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3460-8570","authenticated-orcid":false,"given":"Haibao","family":"Tang","sequence":"first","affiliation":[{"name":"Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology and College of Life Sciences Fujian Agriculture and Forestry University Fuzhou Fujian China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vivek","family":"Krishnakumar","sequence":"additional","affiliation":[{"name":"J. Craig Venter Institute Rockville Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaofei","family":"Zeng","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen Guangdong China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhougeng","family":"Xu","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE) Chinese Academy of Sciences (CAS) Shanghai China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam","family":"Taranto","sequence":"additional","affiliation":[{"name":"School of BioSciences The University of Melbourne Melbourne Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johnathan S.","family":"Lomas","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology University of Nevada Reno Nevada USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yixing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology and College of Life Sciences Fujian Agriculture and Forestry University Fuzhou Fujian China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yumin","family":"Huang","sequence":"additional","affiliation":[{"name":"Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology and College of Life Sciences Fujian Agriculture and Forestry University Fuzhou Fujian China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yibin","family":"Wang","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen Guangdong China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Won Cheol","family":"Yim","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology University of Nevada Reno Nevada USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jisen","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Lab for Conservation and Utilization of Subtropical Agro\u2010Biological Resources, Guangxi Key Lab for Sugarcane Biology Guangxi University Nanning Guangxi China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xingtan","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen Guangdong China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,6,12]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.3148"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-0716-1274-3_4"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/5.3.237"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1104\/pp.111.189514"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09448-8"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.3390\/plants9121706"},{"key":"e_1_2_10_8_1","unstructured":"Armstrong Joel. \u201cEnabling Comparative Genomics at the Scale of Hundreds of Species\u201d Doctoral diss. University of California Santa Cruz Genomics Institute California USA. 2019. 145. PhD. eScholarship. 7pv8w2bz. English.https:\/\/escholarship.org\/uc\/item\/7pv8w2bz"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2023.09.010"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2649-2"},{"key":"e_1_2_10_11_1","doi-asserted-by":"crossref","unstructured":"Rand Knut IvarGrytten MilenaPavlovic ChakravarthiKanduri andGeir KjetilSandve.2022. \u201cBioNumPy: Fast and Easy Analysis of Biological Data With Python.\u201dbioRxiv2022.2012.2021.521373.https:\/\/doi.org\/10.1101\/2022.12.21.521373","DOI":"10.1101\/2022.12.21.521373"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp163"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbp026"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-018-2026-4"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/cgf.13727"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2022.10.018"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0030619"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.113985.110"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1109\/MCSE.2010.118"},{"key":"e_1_2_10_21_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1153917"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1253435"},{"key":"e_1_2_10_23_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-102"},{"key":"e_1_2_10_24_1","doi-asserted-by":"publisher","DOI":"10.1086\/519795"},{"key":"e_1_2_10_25_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0573-1"},{"key":"e_1_2_10_26_1","doi-asserted-by":"publisher","DOI":"10.1002\/0471250953.bi0411s48"},{"key":"e_1_2_10_27_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature10625"},{"key":"e_1_2_10_28_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr944"},{"key":"e_1_2_10_29_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr1293"},{"key":"e_1_2_10_30_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature01521"},{"key":"e_1_2_10_31_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2012-13-1-r3"},{"key":"e_1_2_10_32_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-14998-3"},{"key":"e_1_2_10_33_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.5396706"},{"key":"e_1_2_10_34_1","doi-asserted-by":"publisher","DOI":"10.1155\/2011\/373875"},{"key":"e_1_2_10_35_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ygeno.2019.02.007"},{"key":"e_1_2_10_36_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004509"},{"key":"e_1_2_10_37_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2019.11.011"},{"key":"e_1_2_10_38_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-0716-2561-3_23"},{"key":"e_1_2_10_39_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg112"},{"key":"e_1_2_10_40_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000212"},{"key":"e_1_2_10_41_1","doi-asserted-by":"publisher","DOI":"10.1017\/S0016672311000279"},{"key":"e_1_2_10_42_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-540-24581-0_69"},{"key":"e_1_2_10_43_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41477-019-0487-8"},{"key":"e_1_2_10_44_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02823-7"},{"key":"e_1_2_10_45_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3252"},{"key":"e_1_2_10_46_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.07009"},{"key":"e_1_2_10_47_1","doi-asserted-by":"crossref","unstructured":"Gnerre Sante IainMaccallum DariuszPrzybylski Filipe J.Ribeiro Joshua N.Burton Bruce J.Walker TedSharpe et al.2011. \u201cHigh\u2010Quality Draft Assemblies of Mammalian Genomes From Massively Parallel Sequence Data.\u201dProceedings of the National Academy of Sciences of the United States of America108: 1513\u20131518.https:\/\/doi.org\/10.1073\/pnas.1017351108","DOI":"10.1073\/pnas.1017351108"},{"key":"e_1_2_10_48_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx699"}],"container-title":["iMeta"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/imt2.211","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/imt2.211","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/imt2.211","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T18:21:50Z","timestamp":1785435710000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/imt2.211"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6,12]]},"references-count":47,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2024,8]]}},"alternative-id":["10.1002\/imt2.211"],"URL":"https:\/\/doi.org\/10.1002\/imt2.211","archive":["Portico"],"relation":{},"ISSN":["2770-5986","2770-596X"],"issn-type":[{"value":"2770-5986","type":"print"},{"value":"2770-596X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,6,12]]},"assertion":[{"value":"2024-03-26","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-05-27","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-06-12","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e211"}}