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Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

Alexander Sczyrba, Peter Hofmann, Peter Belmann, David Koslicki, Stefan Janssen, Johannes Dröge, Ivan Gregor, Stephan Majda, Jessika Fiedler, Eik Dahms, Andreas Bremges, Adrian Fritz, Ruben Garrido-Oter, Tue Sparholt Jørgensen, Nicole Shapiro, Philip D. Blood, Alexey Gurevich, Yang Bai, Dmitrij Turaev, Matthew Z. DeMaere, Rayan Chikhi, Niranjan Nagarajan, Christopher Quince, Lars Hestbjerg Hansen, Søren J. Sørensen, Burton K. H. Chia, Bertrand Denis, Jeff L. Froula, Zhong Wang, Robert Egan, Dongwan Don Kang, Jeffrey J. Cook, Charles Deltel, Michael Beckstette, Claire Lemaitre, Pierre Peterlongo, Guillaume Rizk, Dominique Lavenier, Yu-Wei Wu, Steven W. Singer, Chirag Jain, Marc Strous, Heiner Klingenberg, Peter Meinicke, Michael Barton, Thomas Lingner, Hsin-Hung Lin, Yu-Chieh Liao, Genivaldo Gueiros Z. Silva, Daniel A. Cuevas, Robert A. Edwards, Surya Saha, Vitor C. Piro, Bernhard Y. Renard, Mihai Pop, Hans-Peter Klenk, Markus Göker, Nikos Kyrpides, Tanja Woyke, Julia A. Vorholt, Paul Schulze-Lefert, Edward M. Rubin, Aaron E. Darling, Thomas Rattei, Alice C. McHardy
doi: https://doi.org/10.1101/099127
Alexander Sczyrba
1Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, 33594 Germany
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Peter Hofmann
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University, Duesseldorf, 40225 Germany
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, and Braunschweig Integrated Centre of Systems Biology, Braunschweig, 38124 and 38106 Germany
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Peter Belmann
1Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, 33594 Germany
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, and Braunschweig Integrated Centre of Systems Biology, Braunschweig, 38124 and 38106 Germany
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David Koslicki
4Mathematics Department, Oregon State University, Corvallis, OR, 97331 USA
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Stefan Janssen
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, and Braunschweig Integrated Centre of Systems Biology, Braunschweig, 38124 and 38106 Germany
6Departments of Pediatrics and Computer Science and Engineering, University of California, San Diego, CA, 92093 USA
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Johannes Dröge
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University, Duesseldorf, 40225 Germany
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, and Braunschweig Integrated Centre of Systems Biology, Braunschweig, 38124 and 38106 Germany
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Ivan Gregor
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University, Duesseldorf, 40225 Germany
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, and Braunschweig Integrated Centre of Systems Biology, Braunschweig, 38124 and 38106 Germany
9Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, Saarbruecken, 66123 Germany
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Stephan Majda
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University, Duesseldorf, 40225 Germany
8Department of Biology, University of Duisburg and Essen, Essen, 45141 Germany
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Jessika Fiedler
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University, Duesseldorf, 40225 Germany
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, and Braunschweig Integrated Centre of Systems Biology, Braunschweig, 38124 and 38106 Germany
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Eik Dahms
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University, Duesseldorf, 40225 Germany
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, and Braunschweig Integrated Centre of Systems Biology, Braunschweig, 38124 and 38106 Germany
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Andreas Bremges
1Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, 33594 Germany
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, and Braunschweig Integrated Centre of Systems Biology, Braunschweig, 38124 and 38106 Germany
43German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
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Adrian Fritz
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, and Braunschweig Integrated Centre of Systems Biology, Braunschweig, 38124 and 38106 Germany
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Ruben Garrido-Oter
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University, Duesseldorf, 40225 Germany
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, and Braunschweig Integrated Centre of Systems Biology, Braunschweig, 38124 and 38106 Germany
10Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829 Germany
11Cluster of Excellence on Plant Sciences
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Tue Sparholt Jørgensen
14Department of Environmental Science - Environmental microbiology and biotechnology, Aarhus University, Roskilde, 4000 Denmark
15Section of Microbiology, University of Copenhagen, Copenhagen, 2100 Denmark
45Department of Science and Environment, Roskilde University, Roskilde, 4000 Denmark
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Nicole Shapiro
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
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Philip D. Blood
7Pittsburgh Supercomputing Center, Pittsburgh, PA, 15213 USA
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Alexey Gurevich
42Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia, 199034
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Yang Bai
10Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829 Germany
13Current address: Centre of Excellence for Plant and Microbial Sciences (CEPAMS) and State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Science & John Innes Centre, Beijing, 100101, China
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Dmitrij Turaev
41Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, 1090 Austria
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Matthew Z. DeMaere
12The ithree institute, University of Technology of Sydney, Sydney, NSW, 2007 Australia
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Rayan Chikhi
20Department of Computer Science, Research Center in Computer Science (CRIStAL), Signal and Automatic Control of Lille, Lille, 59655 France
21National Centre of the Scientific Research (CNRS), Rennes, 35042 France
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Niranjan Nagarajan
18Department of Computational and Systems Biology, Genome Institute of Singapore, 138672 Singapore
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Christopher Quince
16Department of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, CV4 7AL United Kingdom
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Lars Hestbjerg Hansen
14Department of Environmental Science - Environmental microbiology and biotechnology, Aarhus University, Roskilde, 4000 Denmark
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Søren J. Sørensen
15Section of Microbiology, University of Copenhagen, Copenhagen, 2100 Denmark
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Burton K. H. Chia
18Department of Computational and Systems Biology, Genome Institute of Singapore, 138672 Singapore
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Bertrand Denis
18Department of Computational and Systems Biology, Genome Institute of Singapore, 138672 Singapore
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Jeff L. Froula
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
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Zhong Wang
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
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Robert Egan
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
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Dongwan Don Kang
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
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Jeffrey J. Cook
19Intel Corporation, Hillsboro, OR, 97124 USA
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Charles Deltel
22National Institute of Research in Informatics and Automatics (INRIA), Rennes, 35042 France
23Institute of Research in Informatics and Random Systems (IRISA), Rennes, 35042 France
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Michael Beckstette
17Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, 38124 Germany
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Claire Lemaitre
22National Institute of Research in Informatics and Automatics (INRIA), Rennes, 35042 France
23Institute of Research in Informatics and Random Systems (IRISA), Rennes, 35042 France
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Pierre Peterlongo
22National Institute of Research in Informatics and Automatics (INRIA), Rennes, 35042 France
23Institute of Research in Informatics and Random Systems (IRISA), Rennes, 35042 France
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Guillaume Rizk
23Institute of Research in Informatics and Random Systems (IRISA), Rennes, 35042 France
24Algorizk - IT consulting and software systems, Paris, 75013 France
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Dominique Lavenier
21National Centre of the Scientific Research (CNRS), Rennes, 35042 France
23Institute of Research in Informatics and Random Systems (IRISA), Rennes, 35042 France
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Yu-Wei Wu
25Joint BioEnergy Institute, Emeryville, CA, 94608 USA
44Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
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Steven W. Singer
25Joint BioEnergy Institute, Emeryville, CA, 94608 USA
26Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
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Chirag Jain
27Max Planck Institute for Biology of Ageing, Cologne, 50931 Germany
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Marc Strous
28Energy Engineering and Geomicrobiology, University of Calgary, Calgary, AB T2N 1N4 Canada
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Heiner Klingenberg
29Department of Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, 37077 Germany
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Peter Meinicke
29Department of Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, 37077 Germany
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Michael Barton
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
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Thomas Lingner
30Microarray and Deep Sequencing Core Facility, University Medical Center, Goettingen, 37077 Germany
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Hsin-Hung Lin
31Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, 35053 Taiwan
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Yu-Chieh Liao
31Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, 35053 Taiwan
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Genivaldo Gueiros Z. Silva
32San Diego State University, San Diego, CA, 92182 USA
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Daniel A. Cuevas
32San Diego State University, San Diego, CA, 92182 USA
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Robert A. Edwards
32San Diego State University, San Diego, CA, 92182 USA
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Surya Saha
33Boyce Thompson Institute for Plant Research, New York, 14853 USA
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Vitor C. Piro
34Research Group Bioinformatics, Robert Koch Institute, Berlin, 13353 Germany
35CAPES Foundation, Ministry of Education of Brazil, Brasília, 70040 Brazil
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Bernhard Y. Renard
34Research Group Bioinformatics, Robert Koch Institute, Berlin, 13353 Germany
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Mihai Pop
36Center for Bioinformatics and Computational Biology and Department of Computer Science, University of Maryland, College Park, MD 20742 USA
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Hans-Peter Klenk
37School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU United Kingdom
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Markus Göker
38Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124 Germany
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Nikos Kyrpides
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
39Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
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Tanja Woyke
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
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Julia A. Vorholt
40Swiss Federal Institute of Technology (ETH Zurich), Institute of Microbiology, Zurich, 8093 Switzerland
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Paul Schulze-Lefert
10Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829 Germany
11Cluster of Excellence on Plant Sciences
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Edward M. Rubin
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
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Aaron E. Darling
12The ithree institute, University of Technology of Sydney, Sydney, NSW, 2007 Australia
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Thomas Rattei
41Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, 1090 Austria
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Alice C. McHardy
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University, Duesseldorf, 40225 Germany
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, and Braunschweig Integrated Centre of Systems Biology, Braunschweig, 38124 and 38106 Germany
11Cluster of Excellence on Plant Sciences
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ABSTRACT

In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics complicates proper performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on datasets of unprecedented complexity and realism. Benchmark metagenomes were generated from newly sequenced ~700 microorganisms and ~600 novel viruses and plasmids, including genomes with varying degrees of relatedness to each other and to publicly available ones and representing common experimental setups. Across all datasets, assembly and genome binning programs performed well for species represented by individual genomes, while performance was substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below the family level. Parameter settings substantially impacted performances, underscoring the importance of program reproducibility. While highlighting current challenges in computational metagenomics, the CAMI results provide a roadmap for software selection to answer specific research questions.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted January 09, 2017.
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Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software
Alexander Sczyrba, Peter Hofmann, Peter Belmann, David Koslicki, Stefan Janssen, Johannes Dröge, Ivan Gregor, Stephan Majda, Jessika Fiedler, Eik Dahms, Andreas Bremges, Adrian Fritz, Ruben Garrido-Oter, Tue Sparholt Jørgensen, Nicole Shapiro, Philip D. Blood, Alexey Gurevich, Yang Bai, Dmitrij Turaev, Matthew Z. DeMaere, Rayan Chikhi, Niranjan Nagarajan, Christopher Quince, Lars Hestbjerg Hansen, Søren J. Sørensen, Burton K. H. Chia, Bertrand Denis, Jeff L. Froula, Zhong Wang, Robert Egan, Dongwan Don Kang, Jeffrey J. Cook, Charles Deltel, Michael Beckstette, Claire Lemaitre, Pierre Peterlongo, Guillaume Rizk, Dominique Lavenier, Yu-Wei Wu, Steven W. Singer, Chirag Jain, Marc Strous, Heiner Klingenberg, Peter Meinicke, Michael Barton, Thomas Lingner, Hsin-Hung Lin, Yu-Chieh Liao, Genivaldo Gueiros Z. Silva, Daniel A. Cuevas, Robert A. Edwards, Surya Saha, Vitor C. Piro, Bernhard Y. Renard, Mihai Pop, Hans-Peter Klenk, Markus Göker, Nikos Kyrpides, Tanja Woyke, Julia A. Vorholt, Paul Schulze-Lefert, Edward M. Rubin, Aaron E. Darling, Thomas Rattei, Alice C. McHardy
bioRxiv 099127; doi: https://doi.org/10.1101/099127
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Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software
Alexander Sczyrba, Peter Hofmann, Peter Belmann, David Koslicki, Stefan Janssen, Johannes Dröge, Ivan Gregor, Stephan Majda, Jessika Fiedler, Eik Dahms, Andreas Bremges, Adrian Fritz, Ruben Garrido-Oter, Tue Sparholt Jørgensen, Nicole Shapiro, Philip D. Blood, Alexey Gurevich, Yang Bai, Dmitrij Turaev, Matthew Z. DeMaere, Rayan Chikhi, Niranjan Nagarajan, Christopher Quince, Lars Hestbjerg Hansen, Søren J. Sørensen, Burton K. H. Chia, Bertrand Denis, Jeff L. Froula, Zhong Wang, Robert Egan, Dongwan Don Kang, Jeffrey J. Cook, Charles Deltel, Michael Beckstette, Claire Lemaitre, Pierre Peterlongo, Guillaume Rizk, Dominique Lavenier, Yu-Wei Wu, Steven W. Singer, Chirag Jain, Marc Strous, Heiner Klingenberg, Peter Meinicke, Michael Barton, Thomas Lingner, Hsin-Hung Lin, Yu-Chieh Liao, Genivaldo Gueiros Z. Silva, Daniel A. Cuevas, Robert A. Edwards, Surya Saha, Vitor C. Piro, Bernhard Y. Renard, Mihai Pop, Hans-Peter Klenk, Markus Göker, Nikos Kyrpides, Tanja Woyke, Julia A. Vorholt, Paul Schulze-Lefert, Edward M. Rubin, Aaron E. Darling, Thomas Rattei, Alice C. McHardy
bioRxiv 099127; doi: https://doi.org/10.1101/099127

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