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 Li; 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 Green; David Haussler; Ian Korf; Benedict Paten

doi:10.1101/gr.126599.111

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

Journal article

Open access

Peer reviewed

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, …

Genome research, Vol.21(12), pp.2224-2241

09/16/2011

DOI: https://doi.org/10.1101/gr.126599.111

PMCID: PMC3227110

PMID: 21926179

Abstract

Quantitative Methods

Life Sciences

Bioinformatics

Computer Science

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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Title: Assemblathon 1: A competitive assessment of de novo short read assembly methods
Creators: Dent A. Earl - Center for Biomolecular Science and Engineering
Keith Bradnam - Genome Center [UC Davis]
John St. John - Center for Biomolecular Science and Engineering
Aaron Darling - Genome Center [UC Davis]
Dawei Lin - Genome Center [UC Davis]
Joseph Faas - Genome Center [UC Davis]
Hung On Ken Yu - Genome Center [UC Davis]
Buffalo Vince - Genome Center [UC Davis]
Daniel R. Zerbino - Biomolecular Engineering Department
Mark Diekhans - Biomolecular Engineering Department
Ngan Nguyen - Center for Biomolecular Science and Engineering
Pramila Nuwantha - Computational and Mathematical Biology
Ariyaratne Wing-Kin Sung - Computational and Mathematical Biology
Zemin Ning - The Wellcome Trust Sanger Institute [Cambridge]
Matthias Haimel - European Bioinformatics Institute [Hinxton]
Jared T. Simpson - The Wellcome Trust Sanger Institute [Cambridge]
Nuno A. Fronseca - Center for Research in Advanced Computing Systems
Inanç Birol - Genome Sciences Centre [Vancouver]
T Roderick Docking - Genome Sciences Centre [Vancouver]
Isaac Y. Ho - DOE Joint Genome Institute [Walnut Creek]
Daniel S Rokhsar - DOE Joint Genome Institute [Walnut Creek]
Rayan Chikhi - Biological systems and models, bioinformatics and sequences
Dominique Lavenier - Biological systems and models, bioinformatics and sequences
Guillaume Chapuis - Biological systems and models, bioinformatics and sequences
Delphine Naquin - Biological systems and models, bioinformatics and sequences
Nicolas Maillet - Biological systems and models, bioinformatics and sequences
Michael C. Schatz - Simons Center for Quantitative Biology [Cold Spring Harbor]
David R. Kelly - Center for Bioinformatics and Computational Biology [Maryland]
Adam M. Phillippy - Center for Bioinformatics and Computational Biology [Maryland]
Sergey Koren - Center for Bioinformatics and Computational Biology [Maryland]
Shiaw-Pyng Yang - Monsanto Company
Wei Wu - Monsanto Company
Wen-Chi Chou - Institute of Bioinformatics [Georgia]
Anuj Srivastava - Institute of Bioinformatics [Georgia]
Timothy I. Shaw - Institute of Bioinformatics [Georgia]
J Graham Ruby - Howard Hughes Medical Institute [Chevy Chase]
Peter Skewes-Cox - Department of Biochemistry and Biophysics [San Francisco]
Miguel Betegon - Department of Biochemistry and Biophysics [San Francisco]
Michelle T. Dimon - Department of Biochemistry and Biophysics [San Francisco]
Victor Solovyev - Department of Computer Science [Royal Holloway]
Petr Kosarev - Softberry Inc
Denis Vorobyev - Softberry Inc
Ricardo Ramirez-Gonzalez - The Genome Analysis Centre
Richard Leggett - Sainsbury Laboratory Cambridge
Dan Maclean - Sainsbury Laboratory Cambridge
Fangfang Xia - Computation Institute [Chicago]
Ruibang Luo - Beijing Genomics Institute [Shenzhen]
Zhenyu Li - Beijing Genomics Institute [Shenzhen]
Yinlong Xie - Beijing Genomics Institute [Shenzhen]
Binghang Liu - Beijing Genomics Institute [Shenzhen]
Sante Gnerre - Broad Institute [Cambridge]
Iain Maccallum - Broad Institute [Cambridge]
Dariusz Przybylski - Broad Institute [Cambridge]
Filipe J. Ribeiro - Broad Institute [Cambridge]
Shuangye Yin - Broad Institute [Cambridge]
Ted Sharpe - Broad Institute [Cambridge]
Giles Hall - Broad Institute [Cambridge]
Paul J. Kersey - European Bioinformatics Institute [Hinxton]
Richard Durbin - The Wellcome Trust Sanger Institute [Cambridge]
Shaun D. Jackman - Genome Sciences Centre [Vancouver]
Jarrod A. Chapman - DOE Joint Genome Institute [Walnut Creek]
Xiaoqiu Huang - Department of Computer Science [Ames]
Joseph L. Derisi - Howard Hughes Medical Institute [Chevy Chase]
Mario Caccamo - The Genome Analysis Centre
Yingrui Li - Beijing Genomics Institute [Shenzhen]
David B. Jaffe - Broad Institute [Cambridge]
Richard Green - Biomolecular Engineering Department
David Haussler - Center for Biomolecular Science and Engineering
Ian Korf - Genome Center [UC Davis]
Benedict Paten - Center for Biomolecular Science and Engineering
Publication Details: Genome research, Vol.21(12), pp.2224-2241
Publisher: Cold Spring Harbor Laboratory Press
Identifiers: 9924012913201921
Academic Unit: Department of Biology
Language: English
Resource Type: Journal article

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

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