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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, Fernando Meyer, Monika Balvoit, 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 C. Kyrpides, Tanja Woyke, Julia A. Vorholt, Paul Schulze-Lefert, Edward M. Rubin, Aaron E. Darling, Thomas Rattei, View ORCID ProfileAlice 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 (HHU), Duesseldorf, 40225 Germany
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), and Braunschweig Integrated Centre of Systems Biology (BRICS), 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 (HZI), and Braunschweig Integrated Centre of Systems Biology (BRICS), 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 (HZI), and Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, 38124 and 38106 Germany
5Departments 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 (HHU), Duesseldorf, 40225 Germany
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), and Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, 38124 and 38106 Germany
Ivan Gregor
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, 40225 Germany
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), and Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, 38124 and 38106 Germany
6Department for Computational Genomics and Epidemiology, Max Planck Institute for Informatics, Saarbruecken, 66123 Germany
Stephan Majda
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, 40225 Germany
7Department of Biology, University of Duisburg and Essen, Essen, 45141 Germany
Jessika Fiedler
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, 40225 Germany
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), and Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, 38124 and 38106 Germany
Eik Dahms
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, 40225 Germany
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), and Braunschweig Integrated Centre of Systems Biology (BRICS), 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 (HZI), and Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, 38124 and 38106 Germany
8German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, 38124 Germany
Adrian Fritz
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), and Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, 38124 and 38106 Germany
Ruben Garrido-Oter
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, 40225 Germany
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), and Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, 38124 and 38106 Germany
9Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829 Germany
10Cluster of Excellence on Plant Sciences (CEPLAS)
Tue Sparholt Jørgensen
11Department of Environmental Science - Environmental microbiology and biotechnology, Aarhus University, Roskilde, 4000 Denmark
12Department of Microbiology, University of Copenhagen, Copenhagen, 2100 Denmark
13Department of Science and Environment, Roskilde University, Roskilde, 4000 Denmark
Nicole Shapiro
14Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Philip D. Blood
15Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, 15213 USA
Alexey Gurevich
16Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, 199034 Russia
Yang Bai
9Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829 Germany
17Centre 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
18Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, 1090 Austria
Matthew Z. DeMaere
19The 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
22Department of Computational and Systems Biology, Genome Institute of Singapore, 138672 Singapore
Christopher Quince
23Department of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, CV4 7AL UK
Fernando Meyer
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), and Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, 38124 and 38106 Germany
Monika Balvoit
24Department of Computer Science, University of Tuebingen, Tuebingen, 72076 Germany
Lars Hestbjerg Hansen
11Department of Environmental Science - Environmental microbiology and biotechnology, Aarhus University, Roskilde, 4000 Denmark
Søren J. Sørensen
12Department of Microbiology, University of Copenhagen, Copenhagen, 2100 Denmark
Burton K. H. Chia
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, 40225 Germany
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, 40225 Germany
Bertrand Denis
22Department of Computational and Systems Biology, Genome Institute of Singapore, 138672 Singapore
Jeff L. Froula
14Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Zhong Wang
14Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Robert Egan
14Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Dongwan Don Kang
14Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Jeffrey J. Cook
25Intel Corporation, Hillsboro, OR, 97124 USA
Charles Deltel
26GenScale - Scalable, Optimized and Parallel Algorithms for Genomics, Inria Rennes Bretagne Atlantique,, Rennes, 35042 France
27Institute of Research in Informatics and Random Systems (IRISA), Rennes, 35042 France
Michael Beckstette
28Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, 38124 Germany
Claire Lemaitre
26GenScale - Scalable, Optimized and Parallel Algorithms for Genomics, Inria Rennes Bretagne Atlantique,, Rennes, 35042 France
27Institute of Research in Informatics and Random Systems (IRISA), Rennes, 35042 France
Pierre Peterlongo
26GenScale - Scalable, Optimized and Parallel Algorithms for Genomics, Inria Rennes Bretagne Atlantique,, Rennes, 35042 France
27Institute of Research in Informatics and Random Systems (IRISA), Rennes, 35042 France
Guillaume Rizk
26GenScale - Scalable, Optimized and Parallel Algorithms for Genomics, Inria Rennes Bretagne Atlantique,, Rennes, 35042 France
29Algorizk - IT consulting and software systems, Paris, 75013 France
Dominique Lavenier
21National Centre of the Scientific Research (CNRS), Rennes, 35042 France
27Institute of Research in Informatics and Random Systems (IRISA), Rennes, 35042 France
Yu-Wei Wu
30Joint BioEnergy Institute, Emeryville, CA, 94608 USA
31Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, 110 Taiwan
Steven W. Singer
30Joint BioEnergy Institute, Emeryville, CA, 94608 USA
32Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
Chirag Jain
33School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, 30332 USA
Marc Strous
34Energy Engineering and Geomicrobiology, University of Calgary, Calgary, AB, T2N 1N4 Canada
Heiner Klingenberg
35Department of Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, 37077 Germany
Peter Meinicke
35Department of Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, 37077 Germany
Michael Barton
14Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Thomas Lingner
36Microarray and Deep Sequencing Core Facility, University Medical Center, Goettingen, 37077 Germany
Hsin-Hung Lin
37Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, 35053 Taiwan
Yu-Chieh Liao
37Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, 35053 Taiwan
Genivaldo Gueiros Z. Silva
38San Diego State University, San Diego, CA, 92182 USA
Daniel A. Cuevas
38San Diego State University, San Diego, CA, 92182 USA
Robert A. Edwards
38San Diego State University, San Diego, CA, 92182 USA
Surya Saha
39Boyce Thompson Institute for Plant Research, New York, NY, 14853 USA
Vitor C. Piro
40Research Group Bioinformatics (NG4), Robert Koch Institute, Berlin, 13353 Germany
41Coordination for the Improvement of Higher Education Personnel (CAPES) Foundation, Ministry of Education of Brazil, Brasília, 70040 Brazil
Bernhard Y. Renard
40Research Group Bioinformatics (NG4), Robert Koch Institute, Berlin, 13353 Germany
Mihai Pop
42Center for Bioinformatics and Computational Biology and Department of Computer Science, University of Maryland, College Park, MD, 20742 USA
Hans-Peter Klenk
43School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
Markus Göker
44Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124 Germany
Nikos C. Kyrpides
14Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Tanja Woyke
14Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Julia A. Vorholt
45Institute of Microbiology, Swiss Federal Institute of Technology (ETH Zurich), Zurich, 8093 Switzerland
Paul Schulze-Lefert
9Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829 Germany
10Cluster of Excellence on Plant Sciences (CEPLAS)
Edward M. Rubin
14Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA
Aaron E. Darling
19The ithree institute, University of Technology of Sydney, Sydney, NSW, 2007 Australia
Thomas Rattei
18Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, 1090 Austria
Alice C. McHardy
2Formerly Department for Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, 40225 Germany
3Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), and Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, 38124 and 38106 Germany
10Cluster of Excellence on Plant Sciences (CEPLAS)
Posted June 12, 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, Fernando Meyer, Monika Balvoit, 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 C. 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, Fernando Meyer, Monika Balvoit, 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 C. 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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