دورية أكاديمية
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Assemblathon 1: a competitive assessment of de novo short read assembly methods.

التفاصيل البيبلوغرافية
العنوان: Assemblathon 1: a competitive assessment of de novo short read assembly methods.
المؤلفون: Earl D; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA., Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B
المصدر: Genome research [Genome Res] 2011 Dec; Vol. 21 (12), pp. 2224-41. Date of Electronic Publication: 2011 Sep 16.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
اللغة: English
بيانات الدورية: Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9518021 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-5469 (Electronic) Linking ISSN: 10889051 NLM ISO Abbreviation: Genome Res Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory Press, c1995-
مواضيع طبية MeSH: Genome/*physiology , Genomics/*methods , Sequence Analysis, DNA/*methods
مستخلص: Low-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/.
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معلومات مُعتمدة: F31 HG000064 United States HG NHGRI NIH HHS; R01 HG003474 United States HG NHGRI NIH HHS; United States HHMI Howard Hughes Medical Institute; U41HG004568 United States HG NHGRI NIH HHS; U01HG004695 United States HG NHGRI NIH HHS; 1U24CA143858-01 United States CA NCI NIH HHS; U41 HG004568 United States HG NHGRI NIH HHS; U24 CA143858 United States CA NCI NIH HHS; K22 HG000064 United States HG NHGRI NIH HHS; P41HG002371 United States HG NHGRI NIH HHS; U54 HG004555 United States HG NHGRI NIH HHS; P41 HG002371 United States HG NHGRI NIH HHS; HG00064 United States HG NHGRI NIH HHS; R21 AA022707 United States AA NIAAA NIH HHS; U01 HG004695 United States HG NHGRI NIH HHS; U54HG004555 United States HG NHGRI NIH HHS
تواريخ الأحداث: Date Created: 20110920 Date Completed: 20120325 Latest Revision: 20230203
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC3227110
DOI: 10.1101/gr.126599.111
PMID: 21926179
قاعدة البيانات: MEDLINE
الوصف
تدمد:1549-5469
DOI:10.1101/gr.126599.111