{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T07:56:32Z","timestamp":1773388592607,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,4,26]],"date-time":"2024-04-26T00:00:00Z","timestamp":1714089600000},"content-version":"vor","delay-in-days":30,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Science and Technology Innovation 2030","award":["2023ZD04062"],"award-info":[{"award-number":["2023ZD04062"]}]},{"name":"Major Project of Hubei Hongshan Laboratory","award":["2022HSZD031"],"award-info":[{"award-number":["2022HSZD031"]}]},{"DOI":"10.13039\/501100007925","name":"Huazhong Agricultural University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31821005"],"award-info":[{"award-number":["31821005"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"HZAU Special Funds for Interdisciplinary Scientific Research","award":["SZYJY2022011"],"award-info":[{"award-number":["SZYJY2022011"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Genome assembly remains to be a major task in genomic research. Despite the development over the past decades of different assembly software programs and algorithms, it is still a great challenge to assemble a complete genome without any gaps. With the latest DNA circular consensus sequencing (CCS) technology, several assembly programs can now build a genome from raw sequencing data to contigs; however, some complex sequence regions remain as unresolved gaps. Here, we present a novel gap-filling software, DEGAP (Dynamic Elongation of a Genome Assembly Path), that resolves gap regions by utilizing the dual advantages of accuracy and length of high-fidelity (HiFi) reads. DEGAP identifies differences between reads and provides \u2018GapFiller\u2019 or \u2018CtgLinker\u2019 modes to eliminate or shorten gaps in genomes. DEGAP adopts an iterative elongation strategy that automatically and dynamically adjusts parameters according to three complexity factors affecting the genome to determine the optimal extension path. DEGAP has already been successfully applied to decipher complex genomic regions in several projects and may be widely employed to generate more gap-free genomes.<\/jats:p>","DOI":"10.1093\/bib\/bbae194","type":"journal-article","created":{"date-parts":[[2024,4,26]],"date-time":"2024-04-26T17:49:27Z","timestamp":1714153767000},"source":"Crossref","is-referenced-by-count":5,"title":["DEGAP: Dynamic elongation of a genome assembly path"],"prefix":"10.1093","volume":"25","author":[{"given":"Yicheng","family":"Huang","sequence":"first","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement , Hubei Hongshan Laboratory, , Wuhan 430070 , China"},{"name":"Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University , Hubei Hongshan Laboratory, , Wuhan 430070 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ziyuan","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Pharmacy Practice & Science , College of Pharmacy, , Tucson, AZ 85721 , USA"},{"name":"University of Arizona , College of Pharmacy, , Tucson, AZ 85721 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Monica A","family":"Schmidt","sequence":"additional","affiliation":[{"name":"BIO5 Institute , School of Plant Sciences, , Tucson, AZ 85721 , USA"},{"name":"University of Arizona , School of Plant Sciences, , Tucson, AZ 85721 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Handong","family":"Su","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement , Hubei Hongshan Laboratory, , Wuhan 430070 , China"},{"name":"Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University , Hubei Hongshan Laboratory, , Wuhan 430070 , China"},{"name":"Shenzhen Branch , Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, , Shenzhen 518000 , China"},{"name":"Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, , Shenzhen 518000 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lizhong","family":"Xiong","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement , Hubei Hongshan Laboratory, , Wuhan 430070 , China"},{"name":"Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University , Hubei Hongshan Laboratory, , Wuhan 430070 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8030-5346","authenticated-orcid":false,"given":"Jianwei","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement , Hubei Hongshan Laboratory, , Wuhan 430070 , China"},{"name":"Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University , 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