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

Keith R Bradnam; Joseph N Fass; Anton Alexandrov; Paul Baranay; Michael Bechner; Inanç Birol; Sébastien Boisvert; Jarrod A Chapman; Guillaume Chapuis; Rayan Chikhi; Hamidreza Chitsaz; Wen-Chi Chou; Jacques Corbeil; Cristian Del Fabbro; T Roderick Docking; Richard Durbin; Dent Earl; Scott Emrich; Pavel Fedotov; Nuno A Fonseca; Ganeshkumar Ganapathy; Richard A Gibbs; Sante Gnerre; Élénie Godzaridis; Steve Goldstein; Matthias Haimel; Giles Hall; David Haussler; Joseph B Hiatt; Isaac Y Ho; Jason Howard; Martin Hunt; Shaun D Jackman; David B Jaffe; Erich D Jarvis; Huaiyang Jiang; Sergey Kazakov; Paul J Kersey; Jacob O Kitzman; James R Knight; Sergey Koren; Tak-Wah Lam; Dominique Lavenier; François Laviolette; Yingrui Li; Zhenyu Li; Binghang Liu; Yue Liu; Ruibang Luo; Iain MacCallum; Matthew D MacManes; Nicolas Maillet; Sergey Melnikov; Delphine Naquin; Zemin Ning; Thomas D Otto; Benedict Paten; Octávio S Paulo; Adam M Phillippy; Francisco Pina-Martins; Michael Place; Dariusz Przybylski; Xiang Qin; Carson Qu; Filipe J Ribeiro; Stephen Richards; Daniel S Rokhsar; J Graham Ruby; Simone Scalabrin; Michael C Schatz; David C Schwartz; Alexey Sergushichev; Ted Sharpe; Timothy I Shaw; Jay Shendure; Yujian Shi; Jared T Simpson; Henry Song; Fedor Tsarev; Francesco Vezzi; Riccardo Vicedomini; Bruno M Vieira; Jun Wang; Kim C Worley; Shuangye Yin; Siu-Ming Yiu; Jianying Yuan; Guojie Zhang; Hao Zhang; Shiguo Zhou; Ian F Korf

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

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

Journal article

Peer reviewed

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

Keith R Bradnam, Joseph N Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, Inanç Birol, Sébastien Boisvert, Jarrod A Chapman, Guillaume Chapuis, Rayan Chikhi, …

Gigascience, Vol.2(1), pp.10-10

07/22/2013

DOI: https://doi.org/10.1186/2047-217X-2-10

PMCID: PMC3844414

PMID: 23870653

Abstract

COMPASS

Assessment

N50

Research

Genome assembly

Scaffolds

Heterozygosity

Background The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.

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Title: Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Creators: Keith R Bradnam - Genome Center, UC, Davis, CA 95616, USA
Joseph N Fass - Genome Center, UC, Davis, CA 95616, USA
Anton Alexandrov - National Research University of Information Technology, Mechanics and Optics (University ITMO), St. Petersburg 197101, Russia
Paul Baranay - Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
Michael Bechner - Laboratory for Molecular and Computational Genomics, Departments of Chemistry and Genetics, UW-Biotechnology Center, 425 Henry Mall, Madison, WI 53706, USA
Inanç Birol - Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
Sébastien Boisvert - Infectious Diseases Research Center, Université Laval, Québec, QC G1V 4G2, Canada
Jarrod A Chapman - DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
Guillaume Chapuis - Computer Science department, ENS Cachan/IRISA, 35042 Rennes, France
Rayan Chikhi - Computer Science department, ENS Cachan/IRISA, 35042 Rennes, France
Hamidreza Chitsaz - Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
Wen-Chi Chou - Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
Jacques Corbeil - Infectious Diseases Research Center, Université Laval, Québec, QC G1V 4G2, Canada
Cristian Del Fabbro - IGA, Institute of Applied Genomics, 33100 Udine, Italy
T Roderick Docking - Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
Richard Durbin - The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Dent Earl - Howard Hughes Medical Institute, Center for Biomolecular Science & Engineering, University of California, Santa Cruz, CA 95064 USA
Scott Emrich - Department of Computer Science and Engineering, University of Notre Dame, South Bend, IN 46556, USA
Pavel Fedotov - National Research University of Information Technology, Mechanics and Optics (University ITMO), St. Petersburg 197101, Russia
Nuno A Fonseca - EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Ganeshkumar Ganapathy - Duke University Medical Center, Durham, NC 27710 USA
Richard A Gibbs - Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
Sante Gnerre - Broad Institute, Cambridge, MA 02142, USA
Élénie Godzaridis - Faculty of Medicine, Université Laval, Québec, QC G1V 4G2, Canada
Steve Goldstein - Laboratory for Molecular and Computational Genomics, Departments of Chemistry and Genetics, UW-Biotechnology Center, 425 Henry Mall, Madison, WI 53706, USA
Matthias Haimel - EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Giles Hall - Broad Institute, Cambridge, MA 02142, USA
David Haussler - Howard Hughes Medical Institute, Center for Biomolecular Science & Engineering, University of California, Santa Cruz, CA 95064 USA
Joseph B Hiatt - Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA 98195, USA
Isaac Y Ho - DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
Jason Howard - Duke University Medical Center, Durham, NC 27710 USA
Martin Hunt - The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Shaun D Jackman - Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
David B Jaffe - Broad Institute, Cambridge, MA 02142, USA
Erich D Jarvis - Duke University Medical Center, Durham, NC 27710 USA
Huaiyang Jiang - Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
Sergey Kazakov - National Research University of Information Technology, Mechanics and Optics (University ITMO), St. Petersburg 197101, Russia
Paul J Kersey - EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Jacob O Kitzman - Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA 98195, USA
James R Knight - 454 Life Sciences, 15 Commercial Street, Branford, CT 06405, USA
Sergey Koren - National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702, USA
Tak-Wah Lam - HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Pok Fu Lam Rd, Hong Kong, Hong Kong
Dominique Lavenier - Computer Science department, ENS Cachan/IRISA, 35042 Rennes, France
François Laviolette - Department of Computer Science and Software Engineering, Faculty of Science and Engineering, Université Laval, Québec, QC G1V 4G2, Canada
Yingrui Li - BGI-Shenzhen, Shenzhen, Guangdong 518083, China
Zhenyu Li - BGI-Shenzhen, Shenzhen, Guangdong 518083, China
Binghang Liu - BGI-Shenzhen, Shenzhen, Guangdong 518083, China
Yue Liu - Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
Ruibang Luo - BGI-Shenzhen, Shenzhen, Guangdong 518083, China
Iain MacCallum - Broad Institute, Cambridge, MA 02142, USA
Matthew D MacManes - Berkeley California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
Nicolas Maillet - INRIA, Rennes Bretagne Atlantique, 35042 Rennes, France
Sergey Melnikov - National Research University of Information Technology, Mechanics and Optics (University ITMO), St. Petersburg 197101, Russia
Delphine Naquin - INRIA, Rennes Bretagne Atlantique, 35042 Rennes, France
Zemin Ning - The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Thomas D Otto - The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Benedict Paten - Howard Hughes Medical Institute, Center for Biomolecular Science & Engineering, University of California, Santa Cruz, CA 95064 USA
Octávio S Paulo - Computational Biology & Population Genomics Group, Centre for Environmental Biology, Department of Animal Biology, Faculty of Sciences of the University of Lisbon, Campo Grande, P-1749-016 Lisbon, Portugal
Adam M Phillippy - National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702, USA
Francisco Pina-Martins - Computational Biology & Population Genomics Group, Centre for Environmental Biology, Department of Animal Biology, Faculty of Sciences of the University of Lisbon, Campo Grande, P-1749-016 Lisbon, Portugal
Michael Place - Laboratory for Molecular and Computational Genomics, Departments of Chemistry and Genetics, UW-Biotechnology Center, 425 Henry Mall, Madison, WI 53706, USA
Dariusz Przybylski - Broad Institute, Cambridge, MA 02142, USA
Xiang Qin - Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
Carson Qu - Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
Filipe J Ribeiro - New York Genome Center, New York, NY 10022, USA
Stephen Richards - Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
Daniel S Rokhsar - DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
J Graham Ruby - Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
Simone Scalabrin - IGA, Institute of Applied Genomics, 33100 Udine, Italy
Michael C Schatz - Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
David C Schwartz - Laboratory for Molecular and Computational Genomics, Departments of Chemistry and Genetics, UW-Biotechnology Center, 425 Henry Mall, Madison, WI 53706, USA
Alexey Sergushichev - National Research University of Information Technology, Mechanics and Optics (University ITMO), St. Petersburg 197101, Russia
Ted Sharpe - Broad Institute, Cambridge, MA 02142, USA
Timothy I Shaw - Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
Jay Shendure - Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA 98195, USA
Yujian Shi - BGI-Shenzhen, Shenzhen, Guangdong 518083, China
Jared T Simpson - The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Henry Song - Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
Fedor Tsarev - National Research University of Information Technology, Mechanics and Optics (University ITMO), St. Petersburg 197101, Russia
Francesco Vezzi - Science for Life Laboratory, KTH Royal Institute of Technology, 17121 Solna, Sweden
Riccardo Vicedomini - IGA, Institute of Applied Genomics, 33100 Udine, Italy
Bruno M Vieira - Computational Biology & Population Genomics Group, Centre for Environmental Biology, Department of Animal Biology, Faculty of Sciences of the University of Lisbon, Campo Grande, P-1749-016 Lisbon, Portugal
Jun Wang - BGI-Shenzhen, Shenzhen, Guangdong 518083, China
Kim C Worley - Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
Shuangye Yin - Broad Institute, Cambridge, MA 02142, USA
Siu-Ming Yiu - HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Pok Fu Lam Rd, Hong Kong, Hong Kong
Jianying Yuan - BGI-Shenzhen, Shenzhen, Guangdong 518083, China
Guojie Zhang - BGI-Shenzhen, Shenzhen, Guangdong 518083, China
Hao Zhang - BGI-Shenzhen, Shenzhen, Guangdong 518083, China
Shiguo Zhou - Laboratory for Molecular and Computational Genomics, Departments of Chemistry and Genetics, UW-Biotechnology Center, 425 Henry Mall, Madison, WI 53706, USA
Ian F Korf - Genome Center, UC, Davis, CA 95616, USA
Publication Details: Gigascience, Vol.2(1), pp.10-10
Publisher: BioMed Central
Identifiers: 9924012909301921
Academic Unit: Department of Biology
Language: English
Resource Type: Journal article

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

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