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

Dent Earl, Keith Bradnam, John St. John, Aaron Darling, Dawei Lin, Joseph Fass, Hung On Ken Yu, Vince Buffalo, Daniel R. Zerbino, Mark Diekhans, Ngan Nguyen, Pramila Nuwantha Ariyaratne, Wing Kin Sung, Zemin Ning, Matthias Haimel, Jared T. Simpson, Nuno A. Fonseca, Inanç Birol, T. Roderick Docking, Isaac Y. HoDaniel S. Rokhsar, Rayan Chikhi, Dominique Lavenier, Guillaume Chapuis, Delphine Naquin, Nicolas Maillet, Michael C. Schatz, David R. Kelley, Adam M. Phillippy, Sergey Koren, Shiaw Pyng Yang, Wei Wu, Wen Chi Chou, Anuj Srivastava, Timothy I. Shaw, J. Graham Ruby, Peter Skewes-Cox, Miguel Betegon, Michelle T. Dimon, Victor Solovyev, Igor Seledtsov, Petr Kosarev, Denis Vorobyev, Ricardo Ramirez-Gonzalez, Richard Leggett, Dan MacLean, Fangfang Xia, Ruibang Luo, Zhenyu Li, Yinlong Xie, Binghang Liu, Sante Gnerre, Iain MacCallum, Dariusz Przybylski, Filipe J. Ribeiro, Ted Sharpe, Giles Hall, Paul J. Kersey, Richard Durbin, Shaun D. Jackman, Jarrod A. Chapman, Xiaoqiu Huang, Joseph L. DeRisi, Mario Caccamo, Yingrui Li, David B. Jaffe, Richard E. Green, David Haussler, Ian F Korf, Benedict Paten

Research output: Contribution to journalArticlepeer-review

339 Scopus citations


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

Original languageEnglish (US)
Pages (from-to)2224-2241
Number of pages18
JournalGenome Research
Issue number12
StatePublished - Dec 2011

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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