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Article: Assemblathon 1: A competitive assessment of de novo short read assembly methods

TitleAssemblathon 1: A competitive assessment of de novo short read assembly methods
Authors
Issue Date2011
Citation
Genome Research, 2011, v. 21, n. 12, p. 2224-2241 How to Cite?
AbstractLow-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/. © 2011 by Cold Spring Harbor Laboratory Press.
Persistent Identifierhttp://hdl.handle.net/10722/250980
ISSN
2020 Impact Factor: 9.043
2015 SCImago Journal Rankings: 14.352
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorEarl, Dent-
dc.contributor.authorBradnam, Keith-
dc.contributor.authorSt. John, John-
dc.contributor.authorDarling, Aaron-
dc.contributor.authorLin, Dawei-
dc.contributor.authorFass, Joseph-
dc.contributor.authorYu, Hung On Ken-
dc.contributor.authorBuffalo, Vince-
dc.contributor.authorZerbino, Daniel R.-
dc.contributor.authorDiekhans, Mark-
dc.contributor.authorNguyen, Ngan-
dc.contributor.authorAriyaratne, Pramila Nuwantha-
dc.contributor.authorSung, Wing Kin-
dc.contributor.authorNing, Zemin-
dc.contributor.authorHaimel, Matthias-
dc.contributor.authorSimpson, Jared T.-
dc.contributor.authorFonseca, Nuno A.-
dc.contributor.authorBirol, Inanç-
dc.contributor.authorDocking, T. Roderick-
dc.contributor.authorHo, Isaac Y.-
dc.contributor.authorRokhsar, Daniel S.-
dc.contributor.authorChikhi, Rayan-
dc.contributor.authorLavenier, Dominique-
dc.contributor.authorChapuis, Guillaume-
dc.contributor.authorNaquin, Delphine-
dc.contributor.authorMaillet, Nicolas-
dc.contributor.authorSchatz, Michael C.-
dc.contributor.authorKelley, David R.-
dc.contributor.authorPhillippy, Adam M.-
dc.contributor.authorKoren, Sergey-
dc.contributor.authorYang, Shiaw Pyng-
dc.contributor.authorWu, Wei-
dc.contributor.authorChou, Wen Chi-
dc.contributor.authorSrivastava, Anuj-
dc.contributor.authorShaw, Timothy I.-
dc.contributor.authorRuby, J. Graham-
dc.contributor.authorSkewes-Cox, Peter-
dc.contributor.authorBetegon, Miguel-
dc.contributor.authorDimon, Michelle T.-
dc.contributor.authorSolovyev, Victor-
dc.contributor.authorSeledtsov, Igor-
dc.contributor.authorKosarev, Petr-
dc.contributor.authorVorobyev, Denis-
dc.contributor.authorRamirez-Gonzalez, Ricardo-
dc.contributor.authorLeggett, Richard-
dc.contributor.authorMacLean, Dan-
dc.contributor.authorXia, Fangfang-
dc.contributor.authorLuo, Ruibang-
dc.contributor.authorLi, Zhenyu-
dc.contributor.authorXie, Yinlong-
dc.contributor.authorLiu, Binghang-
dc.contributor.authorGnerre, Sante-
dc.contributor.authorMacCallum, Iain-
dc.contributor.authorPrzybylski, Dariusz-
dc.contributor.authorRibeiro, Filipe J.-
dc.contributor.authorSharpe, Ted-
dc.contributor.authorHall, Giles-
dc.contributor.authorKersey, Paul J.-
dc.contributor.authorDurbin, Richard-
dc.contributor.authorJackman, Shaun D.-
dc.contributor.authorChapman, Jarrod A.-
dc.contributor.authorHuang, Xiaoqiu-
dc.contributor.authorDeRisi, Joseph L.-
dc.contributor.authorCaccamo, Mario-
dc.contributor.authorLi, Yingrui-
dc.contributor.authorJaffe, David B.-
dc.contributor.authorGreen, Richard E.-
dc.contributor.authorHaussler, David-
dc.contributor.authorKorf, Ian-
dc.contributor.authorPaten, Benedict-
dc.date.accessioned2018-02-01T01:54:14Z-
dc.date.available2018-02-01T01:54:14Z-
dc.date.issued2011-
dc.identifier.citationGenome Research, 2011, v. 21, n. 12, p. 2224-2241-
dc.identifier.issn1088-9051-
dc.identifier.urihttp://hdl.handle.net/10722/250980-
dc.description.abstractLow-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/. © 2011 by Cold Spring Harbor Laboratory Press.-
dc.languageeng-
dc.relation.ispartofGenome Research-
dc.titleAssemblathon 1: A competitive assessment of de novo short read assembly methods-
dc.typeArticle-
dc.description.naturelink_to_OA_fulltext-
dc.identifier.doi10.1101/gr.126599.111-
dc.identifier.pmid21926179-
dc.identifier.scopuseid_2-s2.0-83055181941-
dc.identifier.volume21-
dc.identifier.issue12-
dc.identifier.spage2224-
dc.identifier.epage2241-
dc.identifier.eissn1549-5469-
dc.identifier.isiWOS:000297918600021-
dc.identifier.f100013369986-
dc.identifier.issnl1088-9051-

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