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

Dent A. Earl; Keith Bradnam; John St. John; Aaron Darling; Dawei Lin; Joseph Faas; Hung On Ken Yu; Buffalo Vince; Daniel R. Zerbino; Mark Diekhans; Ngan Nguyen; Pramila Nuwantha; Ariyaratne Wing-Kin Sung; Zemin Ning; Matthias Haimel; Jared T. Simpson; Nuno A. Fronseca; Inanç Birol; T. Roderick Docking; Isaac Y. Ho; Daniel S Rokhsar; Rayan Chikhi; Dominique Lavenier; Guillaume Chapuis; Delphine Naquin; Nicolas Maillet; Michael C. Schatz; David R. Kelly; 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; Petr Kosarev; Denis Vorobyev; Ricardo Ramirez-Gonzalez; Richard Leggett; Dan Maclean; Fangfang Xia; Ruibang Luo; Zhenyu L.; Yinlong Xie; Binghang Liu; Sante Gnerre; Iain Maccallum; Dariusz Przybylski; Filipe J. Ribeiro; Shuangye Yin; 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 M. Green; David Haussler; Ian Korf; Benedict Paten

inria-00637571, version 1

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

Dent A. Earl, Keith Bradnam, John St. John, Aaron Darling, Dawei Lin, Joseph Faas, Hung On Ken Yu, Buffalo Vince, Daniel R. Zerbino, Mark Diekhans, Ngan Nguyen, Pramila Nuwantha, Ariyaratne Wing-Kin Sung, Zemin Ning, Matthias Haimel, Jared T. Simpson, Nuno A. Fronseca, Inanç Birol, T. Roderick Docking, Isaac Y. Ho, Daniel S Rokhsar, Rayan Chikhi ()^a^, 1, Dominique Lavenier ¹, Guillaume Chapuis ¹, Delphine Naquin ¹, Nicolas Maillet ¹, Michael C. Schatz, David R. Kelly, 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, Petr Kosarev, Denis Vorobyev, Ricardo Ramirez-Gonzalez, Richard Leggett, Dan Maclean, Fangfang Xia, Ruibang Luo, Zhenyu L., Yinlong Xie, Binghang Liu, Sante Gnerre, Iain Maccallum, Dariusz Przybylski, Filipe J. Ribeiro, Shuangye Yin, 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 M. Green, David Haussler, Ian Korf, Benedict Paten

Genome Research (2011)

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.

a – École normale supérieure de Cachan - ENS Cachan
1: SYMBIOSE (INRIA - IRISA)
CNRS : UMR6074 – INRIA – Institut National des Sciences Appliquées (INSA) - Rennes – Université de Rennes 1

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From: Rayan Chikhi <>
Submitted on: Wednesday, 2 November 2011 13:37:50
Updated on: Monday, 7 November 2011 09:19:47

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DOI: 10.1101/gr.126599.111

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%% inria-00637571, version 1
%% http://hal.inria.fr/inria-00637571
@article{aearl:inria-00637571,
    hal_id = {inria-00637571},
    url = {http://hal.inria.fr/inria-00637571},
    title = {{Assemblathon 1: A competitive assessment of de novo short read assembly methods}},
    author = {A. Earl, Dent and Bradnam, Keith and St. John, John and Darling, Aaron and Lin, Dawei and Faas, Joseph and On Ken Yu, Hung and Vince, Buffalo and R. Zerbino, Daniel and Diekhans, Mark and Nguyen, Ngan and Nuwantha, Pramila and Wing-Kin Sung, Ariyaratne and Ning, Zemin and Haimel, Matthias and T. Simpson, Jared and A. Fronseca, Nuno and Birol, Inan{\c c} and Roderick Docking, T. and Y. Ho, Isaac and S Rokhsar, Daniel and Chikhi, Rayan and Lavenier, Dominique and Chapuis, Guillaume and Naquin, Delphine and Maillet, Nicolas and C. Schatz, Michael and R. Kelly, David and M. Phillippy, Adam and Koren, Sergey and Yang, Shiaw-Pyng and Wu, Wei and Chou, Wen-Chi and Srivastava, Anuj and I. Shaw, Timothy and Graham Ruby, J. and Skewes-Cox, Peter and Betegon, Miguel and T. Dimon, Michelle and Solovyev, Victor and Kosarev, Petr and Vorobyev, Denis and Ramirez-Gonzalez, Ricardo and Leggett, Richard and Maclean, Dan and Xia, Fangfang and Luo, Ruibang and L., Zhenyu and Xie, Yinlong and Liu, Binghang and Gnerre, Sante and Maccallum, Iain and Przybylski, Dariusz and J. Ribeiro, Filipe and Yin, Shuangye and Sharpe, Ted and Hall, Giles and J. Kersey, Paul and Durbin, Richard and D. Jackman, Shaun and A. Chapman, Jarrod and Huang, Xiaoqiu and L. Derisi, Joseph and Caccamo, Mario and Li, Yingrui and B. Jaffe, David and Green, Richard, M. and Haussler, David and Korf, Ian and Paten, Benedict},
    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.}},
    language = {English},
    affiliation = {SYMBIOSE - INRIA - IRISA},
    publisher = {Cold Spring Harbor Laboratory Press},
    journal = {Genome Research},
    note = {International competition of de novo genome assembly. The Symbiose team (IRISA/CNRS/ENS Cachan Brittany) participated to this competition. },
    audience = {international },
    doi = {10.1101/gr.126599.111 },
    year = {2011},
    month = Sep,
}

%F inria-00637571, version 1
%0 Journal Article
%U http://hal.inria.fr/inria-00637571
%2 INFO:INFO_BI;SDV:BIBS
%T Assemblathon 1: A competitive assessment of de novo short read assembly methods
%A A. Earl, Dent
%A Bradnam, Keith
%A St. John, John
%A Darling, Aaron
%A Lin, Dawei
%A Faas, Joseph
%A On Ken Yu, Hung
%A Vince, Buffalo
%A R. Zerbino, Daniel
%A Diekhans, Mark
%A Nguyen, Ngan
%A Nuwantha, Pramila
%A Wing-Kin Sung, Ariyaratne
%A Ning, Zemin
%A Haimel, Matthias
%A T. Simpson, Jared
%A A. Fronseca, Nuno
%A Birol, Inanç
%A Roderick Docking, T.
%A Y. Ho, Isaac
%A S Rokhsar, Daniel
%A Chikhi, Rayan
%A Lavenier, Dominique
%A Chapuis, Guillaume
%A Naquin, Delphine
%A Maillet, Nicolas
%A C. Schatz, Michael
%A R. Kelly, David
%A M. Phillippy, Adam
%A Koren, Sergey
%A Yang, Shiaw-Pyng
%A Wu, Wei
%A Chou, Wen-Chi
%A Srivastava, Anuj
%A I. Shaw, Timothy
%A Graham Ruby, J.
%A Skewes-Cox, Peter
%A Betegon, Miguel
%A T. Dimon, Michelle
%A Solovyev, Victor
%A Kosarev, Petr
%A Vorobyev, Denis
%A Ramirez-Gonzalez, Ricardo
%A Leggett, Richard
%A Maclean, Dan
%A Xia, Fangfang
%A Luo, Ruibang
%A L., Zhenyu
%A Xie, Yinlong
%A Liu, Binghang
%A Gnerre, Sante
%A Maccallum, Iain
%A Przybylski, Dariusz
%A J. Ribeiro, Filipe
%A Yin, Shuangye
%A Sharpe, Ted
%A Hall, Giles
%A J. Kersey, Paul
%A Durbin, Richard
%A D. Jackman, Shaun
%A A. Chapman, Jarrod
%A Huang, Xiaoqiu
%A L. Derisi, Joseph
%A Caccamo, Mario
%A Li, Yingrui
%A B. Jaffe, David
%A Green, Richard
%A Haussler, David
%A Korf, Ian
%A Paten, Benedict
%+ SYMBIOSE - INRIA - IRISA
%X 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.
%G English
%J Genome Research
%8 2011-09-16
%2 international
%I Cold Spring Harbor Laboratory Press
%R 10.1101/gr.126599.111
%Z International competition of de novo genome assembly. The Symbiose team (IRISA/CNRS/ENS Cachan Brittany) participated to this competition.