{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:44:56Z","timestamp":1740185096983,"version":"3.37.3"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2018,9,3]],"date-time":"2018-09-03T00:00:00Z","timestamp":1535932800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61732009","61772557","61622213"],"award-info":[{"award-number":["61732009","61772557","61622213"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100013314","name":"111 Project","doi-asserted-by":"crossref","award":["B18059"],"award-info":[{"award-number":["B18059"]}],"id":[{"id":"10.13039\/501100013314","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Scaffolding is an essential step during the de novo sequence assembly process to infer the direction and order relationships between the contigs and make the sequence assembly results more continuous and complete. However, scaffolding still faces the challenges of repetitive regions in genome, sequencing errors and uneven sequencing depth. Moreover, the accuracy of scaffolding greatly depends on the quality of contigs. Generally, the existing scaffolding methods construct a scaffold graph, and then optimize the graph by deleting spurious edges. Nevertheless, due to the wrong joints between contigs, some correct edges connecting contigs may be deleted.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In this study, we present a novel scaffolding method SCOP, which is the first method to classify the contigs and utilize the vertices and edges to optimize the scaffold graph. Specially, SCOP employs alignment features and GC-content of paired reads to evaluate the quality of contigs (vertices), and divide the contigs into three types (True, Uncertain and Misassembled), and then optimizes the scaffold graph based on the classification of contigs together with the alignment of edges. The experiment results on the datasets of GAGE-A and GAGE-B demonstrate that SCOP performs better than 12 other competing scaffolders.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>SCOP is publicly available for download at https:\/\/github.com\/bioinfomaticsCSU\/SCOP.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty773","type":"journal-article","created":{"date-parts":[[2018,9,1]],"date-time":"2018-09-01T11:43:44Z","timestamp":1535802224000},"page":"1142-1150","source":"Crossref","is-referenced-by-count":10,"title":["SCOP: a novel scaffolding algorithm based on contig classification and optimization"],"prefix":"10.1093","volume":"35","author":[{"given":"Min","family":"Li","sequence":"first","affiliation":[{"name":"Department of computer science, School of Information Science and Engineering, Central South University, Changsha, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li","family":"Tang","sequence":"additional","affiliation":[{"name":"Department of computer science, School of Information Science and Engineering, Central South University, Changsha, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fang-Xiang","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of computer science, School of Information Science and Engineering, Central South University, Changsha, China"},{"name":"Division of Biomedical Engineering, University of Saskatchewan, Saskatoon SK, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Pan","sequence":"additional","affiliation":[{"name":"Department of computer science, School of Information Science and Engineering, Central South University, Changsha, China"},{"name":"Department of Computer Science, Georgia State University, Atlanta, GA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianxin","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of computer science, School of Information Science and Engineering, Central South University, Changsha, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,9,3]]},"reference":[{"key":"2023013107273897400_bty773-B1","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1093\/bioinformatics\/btq626","article-title":"Pe-assembler: de novo assembler using short paired-end reads","volume":"27","author":"Ariyaratne","year":"2011","journal-title":"Bioinformatics"},{"key":"2023013107273897400_bty773-B2","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1093\/bioinformatics\/btv548","article-title":"Scaffoldscaffolder: solving contig orientation via bidirected to directed graph reduction","volume":"32","author":"Bodily","year":"2016","journal-title":"Bioinformatics"},{"key":"2023013107273897400_bty773-B3","doi-asserted-by":"crossref","first-page":"578.","DOI":"10.1093\/bioinformatics\/btq683","article-title":"Scaffolding pre-assembled contigs using sspace","volume":"27","author":"Boetzer","year":"2011","journal-title":"Bioinformatics"},{"key":"2023013107273897400_bty773-B4","doi-asserted-by":"crossref","first-page":"i311.","DOI":"10.1093\/bioinformatics\/bts399","article-title":"Telescoper: de novo assembly of highly repetitive regions","volume":"28","author":"Bresler","year":"2012","journal-title":"Bioinformatics"},{"key":"2023013107273897400_bty773-B5","doi-asserted-by":"crossref","first-page":"345.","DOI":"10.1186\/1471-2105-11-345","article-title":"Sopra: scaffolding algorithm for paired reads via statistical optimization","volume":"11","author":"Dayarian","year":"2010","journal-title":"Bmc Bioinformatics"},{"key":"2023013107273897400_bty773-B6","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1093\/bioinformatics\/bts716","article-title":"Scarpa: scaffolding reads with practical algorithms","volume":"29","author":"Donmez","year":"2013","journal-title":"Bioinformatics"},{"key":"2023013107273897400_bty773-B7","doi-asserted-by":"crossref","first-page":"e1003345","DOI":"10.1371\/journal.pcbi.1003345","article-title":"Next-generation sequence assembly: four stages of data processing and computational challenges","volume":"9","author":"El-Metwally","year":"2013","journal-title":"Plos Comput. 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