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Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

  • Keith R Bradnam1Email author,
  • Joseph N Fass1,
  • Anton Alexandrov36,
  • Paul Baranay2,
  • Michael Bechner39,
  • Inanç Birol33,
  • Sébastien Boisvert10, 11,
  • Jarrod A Chapman20,
  • Guillaume Chapuis7, 9,
  • Rayan Chikhi7, 9,
  • Hamidreza Chitsaz6,
  • Wen-Chi Chou14, 16,
  • Jacques Corbeil10, 13,
  • Cristian Del Fabbro17,
  • T Roderick Docking33,
  • Richard Durbin34,
  • Dent Earl40,
  • Scott Emrich3,
  • Pavel Fedotov36,
  • Nuno A Fonseca30, 35,
  • Ganeshkumar Ganapathy38,
  • Richard A Gibbs32,
  • Sante Gnerre22,
  • Élénie Godzaridis11,
  • Steve Goldstein39,
  • Matthias Haimel30,
  • Giles Hall22,
  • David Haussler40,
  • Joseph B Hiatt41,
  • Isaac Y Ho20,
  • Jason Howard38,
  • Martin Hunt34,
  • Shaun D Jackman33,
  • David B Jaffe22,
  • Erich D Jarvis38,
  • Huaiyang Jiang32,
  • Sergey Kazakov36,
  • Paul J Kersey30,
  • Jacob O Kitzman41,
  • James R Knight37,
  • Sergey Koren24, 25,
  • Tak-Wah Lam29,
  • Dominique Lavenier7, 8, 9,
  • François Laviolette12,
  • Yingrui Li28, 29,
  • Zhenyu Li28,
  • Binghang Liu28,
  • Yue Liu32,
  • Ruibang Luo28, 29,
  • Iain MacCallum22,
  • Matthew D MacManes5,
  • Nicolas Maillet8, 9,
  • Sergey Melnikov36,
  • Delphine Naquin8, 9,
  • Zemin Ning34,
  • Thomas D Otto34,
  • Benedict Paten40,
  • Octávio S Paulo31,
  • Adam M Phillippy24, 25,
  • Francisco Pina-Martins31,
  • Michael Place39,
  • Dariusz Przybylski22,
  • Xiang Qin32,
  • Carson Qu32,
  • Filipe J Ribeiro23,
  • Stephen Richards32,
  • Daniel S Rokhsar20, 21,
  • J Graham Ruby26, 27,
  • Simone Scalabrin17,
  • Michael C Schatz4,
  • David C Schwartz39,
  • Alexey Sergushichev36,
  • Ted Sharpe22,
  • Timothy I Shaw14, 15,
  • Jay Shendure41,
  • Yujian Shi28,
  • Jared T Simpson34,
  • Henry Song32,
  • Fedor Tsarev36,
  • Francesco Vezzi19,
  • Riccardo Vicedomini17, 18,
  • Bruno M Vieira31,
  • Jun Wang28,
  • Kim C Worley32,
  • Shuangye Yin22,
  • Siu-Ming Yiu29,
  • Jianying Yuan28,
  • Guojie Zhang28,
  • Hao Zhang28,
  • Shiguo Zhou39 and
  • Ian F Korf1Email author
Contributed equally
GigaScience20132:10

DOI: 10.1186/2047-217X-2-10

Received: 23 January 2013

Accepted: 15 July 2013

Published: 22 July 2013

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Open Peer Review reports

Pre-publication versions of this article and author comments to reviewers are available by contacting info@biomedcentral.com.

Original Submission
23 Jan 2013 Submitted Original manuscript
Resubmission - Version 2
Submitted Manuscript version 2
Resubmission - Version 3
Submitted Manuscript version 3
Resubmission - Version 4
Submitted Manuscript version 4
11 Feb 2013 Reviewed Reviewer Report - Mick Watson
23 Feb 2013 Reviewed Reviewer Report - C. Titus Brown
19 Jun 2013 Author responded Author comments - Keith Bradnam
Resubmission - Version 5
19 Jun 2013 Submitted Manuscript version 5
25 Jun 2013 Author responded Author comments - Keith Bradnam
Resubmission - Version 6
25 Jun 2013 Submitted Manuscript version 6
28 Jun 2013 Reviewed Reviewer Report - Mick Watson
Resubmission - Version 7
Submitted Manuscript version 7
Publishing
15 Jul 2013 Editorially accepted
22 Jul 2013 Article published 10.1186/2047-217X-2-10

How does Open Peer Review work?

Open peer review is a system where authors know who the reviewers are, and the reviewers know who the authors are. If the manuscript is accepted, the named reviewer reports are published alongside the article.. All previous versions of the manuscript and all author responses to the reviewers are also available.

You can find further information about the peer review system here.

Authors’ Affiliations

(1)
Genome Center
(2)
Computational Biology and Bioinformatics, Yale University
(3)
Department of Computer Science and Engineering, University of Notre Dame
(4)
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory
(5)
Berkeley California Institute for Quantitative Biosciences, University of California
(6)
Department of Computer Science, Wayne State University
(7)
Computer Science department, ENS Cachan/IRISA
(8)
INRIA, Rennes Bretagne Atlantique
(9)
CNRS/Symbiose, IRISA
(10)
Infectious Diseases Research Center, Université Laval
(11)
Faculty of Medicine, Université Laval
(12)
Department of Computer Science and Software Engineering, Faculty of Science and Engineering, Université Laval
(13)
Department of Molecular Medicine, Faculty of Medicine, Université Laval
(14)
Institute of Bioinformatics, University of Georgia
(15)
Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia
(16)
Institute of Aging Research, Hebrew SeniorLife
(17)
IGA, Institute of Applied Genomics
(18)
Department of Mathematics and Computer Science, University of Udine
(19)
Science for Life Laboratory, KTH Royal Institute of Technology
(20)
DOE Joint Genome Institute
(21)
Department of Molecular and Cell Biology, UC Berkeley
(22)
Broad Institute
(23)
New York Genome Center
(24)
National Biodefense Analysis and Countermeasures Center
(25)
Center for Bioinformatics and Computational Biology, University of Maryland
(26)
Department of Biochemistry and Biophysics, University of California
(27)
Howard Hughes Medical Institute
(28)
BGI-Shenzhen
(29)
HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong
(30)
EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus
(31)
Computational Biology & Population Genomics Group, Centre for Environmental Biology, Department of Animal Biology, Faculty of Sciences of the University of Lisbon
(32)
Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine
(33)
Genome Sciences Centre, British Columbia Cancer Agency
(34)
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
(35)
CRACS - INESC TEC
(36)
National Research University of Information Technology, Mechanics and Optics (University ITMO)
(37)
454 Life Sciences
(38)
Duke University Medical Center
(39)
Laboratory for Molecular and Computational Genomics, Departments of Chemistry and Genetics, UW-Biotechnology Center
(40)
Howard Hughes Medical Institute, Center for Biomolecular Science & Engineering, University of California
(41)
Department of Genome Sciences, School of Medicine, University of Washington

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