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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
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
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
David Koslicki
4Mathematics Department, Oregon State University, Corvallis, OR, 97331 USA
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
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
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
Stephan Majda
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University, Duesseldorf, 40225 Germany
8Department of Biology, University of Duisburg and Essen, Essen, 45141 Germany
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
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
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
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
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
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
Nicole Shapiro
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Philip D. Blood
7Pittsburgh Supercomputing Center, Pittsburgh, PA, 15213 USA
Alexey Gurevich
42Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia, 199034
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
Dmitrij Turaev
41Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, 1090 Austria
Matthew Z. DeMaere
12The ithree institute, University of Technology of Sydney, Sydney, NSW, 2007 Australia
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
Niranjan Nagarajan
18Department of Computational and Systems Biology, Genome Institute of Singapore, 138672 Singapore
Christopher Quince
16Department of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, CV4 7AL United Kingdom
Lars Hestbjerg Hansen
14Department of Environmental Science - Environmental microbiology and biotechnology, Aarhus University, Roskilde, 4000 Denmark
Søren J. Sørensen
15Section of Microbiology, University of Copenhagen, Copenhagen, 2100 Denmark
Burton K. H. Chia
18Department of Computational and Systems Biology, Genome Institute of Singapore, 138672 Singapore
Bertrand Denis
18Department of Computational and Systems Biology, Genome Institute of Singapore, 138672 Singapore
Jeff L. Froula
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Zhong Wang
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Robert Egan
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Dongwan Don Kang
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Jeffrey J. Cook
19Intel Corporation, Hillsboro, OR, 97124 USA
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
Michael Beckstette
17Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, 38124 Germany
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
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
Guillaume Rizk
23Institute of Research in Informatics and Random Systems (IRISA), Rennes, 35042 France
24Algorizk - IT consulting and software systems, Paris, 75013 France
Dominique Lavenier
21National Centre of the Scientific Research (CNRS), Rennes, 35042 France
23Institute of Research in Informatics and Random Systems (IRISA), Rennes, 35042 France
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
Steven W. Singer
25Joint BioEnergy Institute, Emeryville, CA, 94608 USA
26Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
Chirag Jain
27Max Planck Institute for Biology of Ageing, Cologne, 50931 Germany
Marc Strous
28Energy Engineering and Geomicrobiology, University of Calgary, Calgary, AB T2N 1N4 Canada
Heiner Klingenberg
29Department of Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, 37077 Germany
Peter Meinicke
29Department of Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, 37077 Germany
Michael Barton
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Thomas Lingner
30Microarray and Deep Sequencing Core Facility, University Medical Center, Goettingen, 37077 Germany
Hsin-Hung Lin
31Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, 35053 Taiwan
Yu-Chieh Liao
31Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, 35053 Taiwan
Genivaldo Gueiros Z. Silva
32San Diego State University, San Diego, CA, 92182 USA
Daniel A. Cuevas
32San Diego State University, San Diego, CA, 92182 USA
Robert A. Edwards
32San Diego State University, San Diego, CA, 92182 USA
Surya Saha
33Boyce Thompson Institute for Plant Research, New York, 14853 USA
Vitor C. Piro
34Research Group Bioinformatics, Robert Koch Institute, Berlin, 13353 Germany
35CAPES Foundation, Ministry of Education of Brazil, Brasília, 70040 Brazil
Bernhard Y. Renard
34Research Group Bioinformatics, Robert Koch Institute, Berlin, 13353 Germany
Mihai Pop
36Center for Bioinformatics and Computational Biology and Department of Computer Science, University of Maryland, College Park, MD 20742 USA
Hans-Peter Klenk
37School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU United Kingdom
Markus Göker
38Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124 Germany
Nikos Kyrpides
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
39Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
Tanja Woyke
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Julia A. Vorholt
40Swiss Federal Institute of Technology (ETH Zurich), Institute of Microbiology, Zurich, 8093 Switzerland
Paul Schulze-Lefert
10Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829 Germany
11Cluster of Excellence on Plant Sciences
Edward M. Rubin
5Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Aaron E. Darling
12The ithree institute, University of Technology of Sydney, Sydney, NSW, 2007 Australia
Thomas Rattei
41Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, 1090 Austria
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
Article usage
Posted January 09, 2017.
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
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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