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

Dent A. Earl 1, 2 Keith Bradnam 3 John St. John 1, 2 Aaron Darling 3 Dawei Lin 3, 4 Joseph Faas 3, 4 Hung On Ken Yu 3 Buffalo Vince 3, 4 Daniel R. Zerbino 2 Mark Diekhans 2, 1 Ngan Nguyen 1, 2 Pramila Nuwantha 5 Ariyaratne Wing-Kin Sung 5, 6 Zemin Ning 7 Matthias Haimel 8 Jared T. Simpson 7 Nuno A. Fronseca 9 Inanç Birol 10 T. Roderick Docking 10 Isaac Y. Ho 11 Daniel S Rokhsar 11, 12 Rayan Chikhi 13 Dominique Lavenier 13 Guillaume Chapuis 13 Delphine Naquin 13 Nicolas Maillet 13 Michael C. Schatz 14 David R. Kelly 15 Adam M. Phillippy 15, 16 Sergey Koren 15, 16 Shiaw-Pyng Yang 17 Wei Wu 17 Wen-Chi Chou 18 Anuj Srivastava 18 Timothy I. Shaw 18 J. Graham Ruby 19, 20 Peter Skewes-Cox 20, 19, 21 Miguel Betegon 20, 19 Michelle T. Dimon 20, 19 Victor Solovyev 22 Petr Kosarev 23 Denis Vorobyev 23 Ricardo Ramirez-Gonzalez 24 Richard Leggett 25 Dan Maclean 25 Fangfang Xia 26 Ruibang Luo 27 Zhenyu Li 27 Yinlong Xie 27 Binghang Liu 27 Sante Gnerre 28 Iain Maccallum 28 Dariusz Przybylski 28 Filipe J. Ribeiro 28 Shuangye Yin 28 Ted Sharpe 28 Giles Hall 28 Paul J. Kersey 8 Richard Durbin 7 Shaun D. Jackman 10 Jarrod A. Chapman 11 Xiaoqiu Huang 29 Joseph L. Derisi 19, 21 Mario Caccamo 24 Yingrui Li 27 David B. Jaffe 28 Richard Green 2 David Haussler 1, 2, 19 Ian Korf 3 Benedict Paten 1, 2, 19
Abstract : Low cost short read sequencing technology has revolutionised 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 dataset 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.
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Article dans une revue
Genome Research, Cold Spring Harbor Laboratory Press, 2011, 〈10.1101/gr.126599.111〉
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Soumis le : mercredi 2 novembre 2011 - 13:37:50
Dernière modification le : dimanche 25 novembre 2018 - 14:28:09

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Dent A. Earl, Keith Bradnam, John St. John, Aaron Darling, Dawei Lin, et al.. Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research, Cold Spring Harbor Laboratory Press, 2011, 〈10.1101/gr.126599.111〉. 〈inria-00637571〉

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