{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T15:00:01Z","timestamp":1780326001662,"version":"3.54.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,10,26]],"date-time":"2016-10-26T00:00:00Z","timestamp":1477440000000},"content-version":"vor","delay-in-days":131,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Next generation sequencing technologies have revolutionized our ability to rapidly and affordably generate vast quantities of sequence data. Once generated, raw sequences are assembled into contigs or scaffolds. However, these assemblies are mostly fragmented and inaccurate at the whole genome scale, largely due to the inability to integrate additional informative datasets (e.g. physical, optical and genetic maps). To address this problem, we developed a semi-automated software tool\u2014Genome Puzzle Master (GPM)\u2014that enables the integration of additional genomic signposts to edit and build \u2018new-gen-assemblies\u2019 that result in high-quality \u2018annotation-ready\u2019 pseudomolecules.<\/jats:p>\n               <jats:p>Results: With GPM, loaded datasets can be connected to each other via their logical relationships which accomplishes tasks to \u2018group,\u2019 \u2018merge,\u2019 \u2018order and orient\u2019 sequences in a draft assembly. Manual editing can also be performed with a user-friendly graphical interface. Final pseudomolecules reflect a user\u2019s total data package and are available for long-term project management. GPM is a web-based pipeline and an important part of a Laboratory Information Management System (LIMS) which can be easily deployed on local servers for any genome research laboratory.<\/jats:p>\n               <jats:p>Availability and Implementation: The GPM (with LIMS) package is available at https:\/\/github.com\/Jianwei-Zhang\/LIMS<\/jats:p>\n               <jats:p>Contacts: \u00a0jzhang@mail.hzau.edu.cn or rwing@mail.arizona.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw370","type":"journal-article","created":{"date-parts":[[2016,6,19]],"date-time":"2016-06-19T00:18:20Z","timestamp":1466295500000},"page":"3058-3064","source":"Crossref","is-referenced-by-count":28,"title":["Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences"],"prefix":"10.1093","volume":"32","author":[{"given":"Jianwei","family":"Zhang","sequence":"first","affiliation":[{"name":"1 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China"},{"name":"2 Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dave","family":"Kudrna","sequence":"additional","affiliation":[{"name":"2 Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting","family":"Mu","sequence":"additional","affiliation":[{"name":"1 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiming","family":"Li","sequence":"additional","affiliation":[{"name":"1 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dario","family":"Copetti","sequence":"additional","affiliation":[{"name":"2 Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA"},{"name":"3 International Rice Research Institute, Genetic Resource Center, Los Ba\u00f1os, Laguna, Philippines"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yeisoo","family":"Yu","sequence":"additional","affiliation":[{"name":"2 Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose Luis","family":"Goicoechea","sequence":"additional","affiliation":[{"name":"2 Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Lei","sequence":"additional","affiliation":[{"name":"1 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rod A.","family":"Wing","sequence":"additional","affiliation":[{"name":"2 Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA"},{"name":"3 International Rice Research Institute, Genetic Resource Center, Los Ba\u00f1os, Laguna, Philippines"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,6,17]]},"reference":[{"key":"2023020113451694800_btw370-B1","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/nmeth.1527","article-title":"Limitations of next-generation genome sequence assembly","volume":"8","author":"Alkan","year":"2011","journal-title":"Nat. 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