دورية أكاديمية
Assemblathon 1: a competitive assessment of de novo short read assembly methods.
العنوان: | Assemblathon 1: a competitive assessment of de novo short read assembly methods. |
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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/. |
References: | Genome Res. 2008 Feb;18(2):324-30. (PMID: 18083777) Genome Res. 2004 Apr;14(4):708-15. (PMID: 15060014) BMC Genomics. 2009 Apr 24;10:180. (PMID: 19393050) Curr Opin Genet Dev. 2006 Dec;16(6):545-52. (PMID: 17055251) Nature. 2008 Apr 24;452(7190):991-6. (PMID: 18432245) Bioinformatics. 2007 Feb 15;23(4):500-1. (PMID: 17158514) Genome Res. 2007 Nov;17(11):1697-706. (PMID: 17908823) Bioinformatics. 2007 Nov 1;23(21):2942-4. (PMID: 17893086) Trends Genet. 2008 Mar;24(3):142-9. (PMID: 18262676) Bioinformatics. 2010 Jun 15;26(12):i367-73. (PMID: 20529929) Genome Res. 2003 Jan;13(1):81-90. (PMID: 12529309) Bioinformatics. 2005 Sep 1;21 Suppl 2:ii79-85. (PMID: 16204131) Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82. (PMID: 20959295) Genome Biol. 2009 Feb 23;10(2):R23. (PMID: 19236709) PLoS One. 2010 Jun 25;5(6):e11147. (PMID: 20593022) Nat Rev Genet. 2010 Jan;11(1):31-46. (PMID: 19997069) Science. 2011 Feb 4;331(6017):555-61. (PMID: 21292972) PLoS One. 2011 Feb 14;6(2):e17034. (PMID: 21340033) Nature. 2005 Dec 8;438(7069):803-19. (PMID: 16341006) PLoS One. 2011 Apr 29;6(4):e19175. (PMID: 21559467) Genome Res. 2009 May;19(5):943-57. (PMID: 19218533) Genome Res. 2008 May;18(5):802-9. (PMID: 18332092) Genome Res. 2008 May;18(5):821-9. (PMID: 18349386) Genome Biol. 2008;9(3):R55. (PMID: 18341692) Nature. 2011 Jan 27;469(7331):529-33. (PMID: 21270892) J Comput Biol. 1995 Summer;2(2):275-90. (PMID: 7497129) Nature. 2010 Jan 21;463(7279):311-7. (PMID: 20010809) Genome Biol. 2009;10(10):R103. (PMID: 19796385) PLoS One. 2011 Mar 14;6(3):e17915. (PMID: 21423806) PLoS Biol. 2009 May 5;7(5):e1000112. (PMID: 19468303) Genome Res. 2010 Feb;20(2):265-72. (PMID: 20019144) J Comput Biol. 2009 Aug;16(8):1101-16. (PMID: 19645596) Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6466-70. (PMID: 16614066) Nature. 2005 Sep 15;437(7057):376-80. (PMID: 16056220) Nucleic Acids Res. 2009 Jan;37(1):289-97. (PMID: 19042974) Genome Res. 2010 May;20(5):675-84. (PMID: 20305016) Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9748-53. (PMID: 11504945) Bioinformatics. 2006 Dec 1;22(23):2971-2. (PMID: 17021158) Nat Methods. 2011 Jan;8(1):61-5. (PMID: 21102452) Genome Res. 2002 Jan;12(1):177-89. (PMID: 11779843) Nat Biotechnol. 2009 May;27(5):455-7. (PMID: 19430453) Science. 2001 Feb 16;291(5507):1304-51. (PMID: 11181995) PLoS One. 2011;6(8):e23501. (PMID: 21876754) Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7. (PMID: 271968) J Comput Biol. 2011 Mar;18(3):469-81. (PMID: 21385048) Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1513-8. (PMID: 21187386) PLoS Comput Biol. 2009 Jul;5(7):e1000432. (PMID: 19593373) Science. 2010 May 7;328(5979):710-722. (PMID: 20448178) Nature. 2010 Jan 21;463(7279):303-4. (PMID: 20090741) BMC Genomics. 2008 Oct 31;9:517. (PMID: 18976482) Nature. 2001 Feb 15;409(6822):860-921. (PMID: 11237011) Nature. 2004 Apr 1;428(6982):522-8. (PMID: 15057823) Bioinformatics. 2009 Aug 15;25(16):2078-9. (PMID: 19505943) J Comput Biol. 2006 Mar;13(2):567-78. (PMID: 16597257) Genome Res. 2008 May;18(5):810-20. (PMID: 18340039) Genome Res. 2011 Sep;21(9):1512-28. (PMID: 21665927) Genome Res. 1998 Mar;8(3):175-85. (PMID: 9521921) Bioinformatics. 2011 Aug 1;27(15):2031-7. (PMID: 21636596) Genome Biol. 2010;11(11):R116. (PMID: 21114842) Genome Res. 2009 Jun;19(6):1117-23. (PMID: 19251739) Genomics. 2010 Jun;95(6):315-27. (PMID: 20211242) Genome Res. 2009 Feb;19(2):336-46. (PMID: 19056694) J Comput Biol. 1998 Fall;5(3):493-504. (PMID: 9773345) BMC Bioinformatics. 2008 Jan 09;9:11. (PMID: 18184432) J Mol Biol. 1990 Oct 5;215(3):403-10. (PMID: 2231712) PLoS One. 2008 Oct 08;3(10):e3373. (PMID: 18841204) Science. 2000 Mar 24;287(5461):2196-204. (PMID: 10731133) Science. 2009 Jan 2;323(5910):133-8. (PMID: 19023044) Nature. 2002 Dec 5;420(6915):520-62. (PMID: 12466850) |
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 |
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