{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,1,4]],"date-time":"2025-01-04T05:26:47Z","timestamp":1735968407393,"version":"3.32.0"},"reference-count":49,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2020,9,1]],"date-time":"2020-09-01T00:00:00Z","timestamp":1598918400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2020,9,1]],"date-time":"2020-09-01T00:00:00Z","timestamp":1598918400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2020,9,1]],"date-time":"2020-09-01T00:00:00Z","timestamp":1598918400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Quant. Biol."],"published-print":{"date-parts":[[2020,9]]},"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>The single\u2010molecular sequencing (SMS) is under rapid development and generating increasingly long and accurate sequences. <jats:italic>De novo<\/jats:italic> assembly of genomes from SMS sequences is a critical step for many genomic studies. To scale well with the developing trends of SMS, many <jats:italic>de novo<\/jats:italic> assemblers for SMS have been released. These assembly workflows can be categorized into two different kinds: the correction\u2010and\u2010assembly strategy and the assembly\u2010and\u2010correction strategy, both of which are gaining more and more attentions.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In this article we make a discussion on the characteristics of errors in SMS sequences. We then review the currently widely applied <jats:italic>de novo<\/jats:italic> assemblers for SMS sequences. We also describe computational methods relevant to <jats:italic>de novo<\/jats:italic> assembly, including the alignment methods and the error correction methods. Benchmarks are provided to analyze their performance on different datasets and to provide use guides on applying the computation methods.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>We make a detailed review on the latest development of <jats:italic>de novo<\/jats:italic> assembly and some relevant algorithms for SMS, including their rationales, solutions and results. Besides, we provide use guides on the algorithms based on their benchmark results. Finally we conclude the review by giving some developing trends of third generation sequencing (TGS).<\/jats:p><\/jats:sec>","DOI":"10.1007\/s40484-020-0214-5","type":"journal-article","created":{"date-parts":[[2020,9,14]],"date-time":"2020-09-14T13:03:10Z","timestamp":1600088590000},"page":"203-215","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["A survey on <i>de novo<\/i> assembly methods for single\u2010molecular sequencing"],"prefix":"10.1002","volume":"8","author":[{"given":"Ying","family":"Chen","sequence":"first","affiliation":[{"name":"State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat\u2010Sen University Guangzhou 510275 China"}]},{"given":"Chuan\u2010Le","family":"Xiao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat\u2010Sen University Guangzhou 510275 China"}]}],"member":"311","published-online":{"date-parts":[[2020,9]]},"reference":[{"key":"e_1_2_9_2_2","doi-asserted-by":"publisher","DOI":"10.1186\/1754\u20106834\u20107\u201040"},{"key":"e_1_2_9_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.gpb.2015.08.002"},{"key":"e_1_2_9_4_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1162986"},{"key":"e_1_2_9_5_2","doi-asserted-by":"publisher","DOI":"10.1533\/9780857099167.1.3"},{"key":"e_1_2_9_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587\u2010019\u20100217\u20109"},{"key":"e_1_2_9_7_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2474"},{"key":"e_1_2_9_8_2","first-page":"1256","article-title":"Nanopore sequencing data analysis: state of the art, applications and challenges.","volume":"19","author":"Magi A.","year":"2018","journal-title":"Brief. Bioinformatics"},{"key":"e_1_2_9_9_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4060"},{"key":"e_1_2_9_10_2","first-page":"940","article-title":"Characterization of MinION nanopore data for resequencing analyses.","volume":"18","author":"Magi A.","year":"2017","journal-title":"Brief. Bioinformatics"},{"key":"e_1_2_9_11_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059\u2010018\u20101462\u20109"},{"key":"e_1_2_9_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3444"},{"key":"e_1_2_9_13_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0112963"},{"key":"e_1_2_9_14_2","doi-asserted-by":"publisher","DOI":"10.3390\/genes10010062"},{"key":"e_1_2_9_15_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.214270.116"},{"key":"e_1_2_9_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2288"},{"key":"e_1_2_9_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2280"},{"key":"e_1_2_9_18_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.141515.112"},{"key":"e_1_2_9_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2474"},{"key":"e_1_2_9_20_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022\u20102836(81)90087\u20105"},{"key":"e_1_2_9_21_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.17.3389"},{"key":"e_1_2_9_22_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102105\u201013\u2010238"},{"key":"e_1_2_9_23_2","doi-asserted-by":"crossref","unstructured":"Ferragina P.andManzini G.(2000)Opportunistic data structures with applications In: Proceedings the 41st Annual Symposium on Foundations of Computer Science pp.390\u2013398. IEEE","DOI":"10.1109\/SFCS.2000.892127"},{"key":"e_1_2_9_24_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp698"},{"key":"e_1_2_9_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_2_9_26_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv784"},{"key":"e_1_2_9_27_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn032"},{"key":"e_1_2_9_28_2","doi-asserted-by":"crossref","unstructured":"Abouelhoda M. I.andOhlebusch E.A. (2003)Local chaining algorithm and its applications in comparative genomics. In: International Workshop on Algorithms in Bioinformatics pp. 1\u201316. Berlin: Springer","DOI":"10.1007\/978-3-540-39763-2_1"},{"key":"e_1_2_9_29_2","doi-asserted-by":"publisher","DOI":"10.1145\/146637.146650"},{"key":"e_1_2_9_30_2","doi-asserted-by":"crossref","unstructured":"Myers G.(2014)Efficient local alignment discovery amongst noisy long reads In: International Workshop on Algorithms in Bioinformatics pp.52\u201367. Berlin: Springer","DOI":"10.1007\/978-3-662-44753-6_5"},{"key":"e_1_2_9_31_2","unstructured":"Cormen T. H. Leiserson C. E. Rivest R. L.andStein C.(2009)Introduction to Algorithms (3rd. edition) pp.197\u2013204. Cambridge: MIT Press"},{"key":"e_1_2_9_32_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF01840446"},{"key":"e_1_2_9_33_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bth408"},{"key":"e_1_2_9_34_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw152"},{"key":"e_1_2_9_35_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"e_1_2_9_36_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0092\u20108240(05)80216\u20102"},{"key":"e_1_2_9_37_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12859\u2010018\u20102014\u20108"},{"key":"e_1_2_9_38_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw753"},{"key":"e_1_2_9_39_2","doi-asserted-by":"publisher","DOI":"10.1145\/316542.316550"},{"key":"e_1_2_9_40_2","doi-asserted-by":"publisher","DOI":"10.1145\/360825.360861"},{"key":"e_1_2_9_41_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/18.3.452"},{"key":"e_1_2_9_42_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4035"},{"key":"e_1_2_9_43_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti1114"},{"key":"e_1_2_9_44_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3238"},{"key":"e_1_2_9_45_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.215087.116"},{"key":"e_1_2_9_46_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn548"},{"key":"e_1_2_9_47_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4432"},{"key":"e_1_2_9_48_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587\u2010019\u20100072\u20108"},{"key":"e_1_2_9_49_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010019\u20100669\u20103"},{"key":"e_1_2_9_50_2","doi-asserted-by":"crossref","unstructured":"Chen Y. Nie F. Xie S.\u2010Q.andZheng Y.\u2010F.(2020)Fast and accurate assembly of Nanopore reads via progressive error correction and adaptive read selection.bioRxiv 930107","DOI":"10.1101\/2020.02.01.930107"}],"container-title":["Quantitative Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s40484-020-0214-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s40484-020-0214-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s40484-020-0214-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1007\/s40484-020-0214-5","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,3]],"date-time":"2025-01-03T09:52:10Z","timestamp":1735897930000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1007\/s40484-020-0214-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,9]]},"references-count":49,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2020,9]]}},"alternative-id":["10.1007\/s40484-020-0214-5"],"URL":"https:\/\/doi.org\/10.1007\/s40484-020-0214-5","archive":["Portico"],"relation":{},"ISSN":["2095-4689","2095-4697"],"issn-type":[{"type":"print","value":"2095-4689"},{"type":"electronic","value":"2095-4697"}],"subject":[],"published":{"date-parts":[[2020,9]]},"assertion":[{"value":"10 March 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 May 2020","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 June 2020","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 September 2020","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"This content has been made available to all.","name":"free","label":"Free to read"}]}}