Title :

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

Author(s) :

Sczyrba, Alexander [Auteur correspondant]
Center for Biotechnology [CeBiTec]
Technische Fakultät, Universität Bielefeld
Hofmann, Peter [Auteur]
Algorithmische Bioinformatik [Düsseldorf]
Computational Biology of Infection Research [Braunschweig]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Belmann, Peter [Auteur]
Center for Biotechnology [CeBiTec]
Computational Biology of Infection Research [Braunschweig]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Koslicki, David [Auteur]
Department of Mathematics [Corvallis, Oregon]
Janssen, Stefan [Auteur]
Computational Biology of Infection Research [Braunschweig]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Department of Computer Science and Engineering [Univ California San Diego] [CSE - UC San Diego]
Department of Pediatrics [Univ California San Diego] [UC San Diego]
Dröge, Johannes [Auteur]
Algorithmische Bioinformatik [Düsseldorf]
Computational Biology of Infection Research [Braunschweig]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Gregor, Ivan [Auteur]
Algorithmische Bioinformatik [Düsseldorf]
Max Planck Institute for Informatics [Saarbrücken]
Majda, Stephan [Auteur]
Algorithmische Bioinformatik [Düsseldorf]
Faculty of Biology [Essen]
Fiedler, Jessika [Auteur]
Algorithmische Bioinformatik [Düsseldorf]
Computational Biology of Infection Research [Braunschweig]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Dahms, Eik [Auteur]
Algorithmische Bioinformatik [Düsseldorf]
Computational Biology of Infection Research [Braunschweig]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Bremges, Andreas [Auteur]
Center for Biotechnology [CeBiTec]
Technische Fakultät, Universität Bielefeld
German Center for Infection Research - partner site Hannover-Braunschweig [DZIF]
Computational Biology of Infection Research [Braunschweig]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Fritz, Adrian [Auteur]
Computational Biology of Infection Research [Braunschweig]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Garrido-Oter, Ruben [Auteur]
Algorithmische Bioinformatik [Düsseldorf]
Department of Plant Microbe Interactions
Cluster of Excellence on Plant Sciences [CEPLAS]
Jørgensen, Tue Sparholt [Auteur]
Department of Environmental Science [Roskilde] [ENVS]
Section of Microbiology [Copenhagen]
Department of Science and Environment [Roskilde]
Shapiro, Nicole [Auteur]
DOE Joint Genome Institute [Walnut Creek]
Blood, Philip D [Auteur]
Pittsburgh Supercomputing Center [PSC]
Gurevich, Alexey [Auteur]
Center for Algorithmic Biotechnology [Saint Petersburg]
Bai, Yang [Auteur]
Department of Plant Microbe Interactions
Centre of Excellence for Plant and Microbial Sciences [CEPAMS]
Turaev, Dmitrij [Auteur]
Department of Microbiology and Ecosystem Science [Vienna]
Demaere, Matthew Z [Auteur]
iThree Institute
Chikhi, Rayan [Auteur]
Bioinformatics and Sequence Analysis [BONSAI]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Nagarajan, Niranjan [Auteur]
Department of Computational and Systems Biology [Singapore]
Quince, Christopher [Auteur]
Department of Microbiology and Infection [Coventry]
Hansen, Lars Hestbjerg [Auteur]
Department of Environmental Science [Roskilde] [ENVS]
Sørensen, Søren J [Auteur]
Section of Microbiology [Copenhagen]
Chia, Burton K H [Auteur]
Department of Computational and Systems Biology [Singapore]
Denis, Bertrand [Auteur]
Department of Computational and Systems Biology [Singapore]
Froula, Jeff L [Auteur]
DOE Joint Genome Institute [Walnut Creek]
Wang, Zhong [Auteur]
DOE Joint Genome Institute [Walnut Creek]
Egan, Robert [Auteur]
DOE Joint Genome Institute [Walnut Creek]
Don Kang, Dongwan [Auteur]
DOE Joint Genome Institute [Walnut Creek]
Cook, Jeffrey J [Auteur]
Intel Corporation [Hillsboro]
Deltel, Charles [Auteur]
Scalable, Optimized and Parallel Algorithms for Genomics [GenScale]
Beckstette, Michael [Auteur]
Department of Molecular Infection Biology [Braunschweig]
Lemaitre, Claire [Auteur]
Scalable, Optimized and Parallel Algorithms for Genomics [GenScale]
Peterlongo, Peter [Auteur]
Scalable, Optimized and Parallel Algorithms for Genomics [GenScale]
Rizk, Guillaume [Auteur]
Scalable, Optimized and Parallel Algorithms for Genomics [GenScale]
Lavenier, Dominique [Auteur]
Scalable, Optimized and Parallel Algorithms for Genomics [GenScale]
Wu, Yu-Wei [Auteur]
Joint BioEnergy Institute [Emeryville]
Graduate Institute of Biomedical Informatics [Taipei]
Singer, Steven W [Auteur]
Joint BioEnergy Institute [Emeryville]
Biological Systems and Engineering [LBNL Berkeley]
Jain, Chirag [Auteur]
Max planck Institute for Biology of Ageing [Cologne]
Strous, Marc [Auteur]
Energy Engineering and Geomicrobiology [Calgary]
Klingenberg, Heiner [Auteur]
Institute of Microbiology and Genetics [Göttingen]
Meinicke, Peter [Auteur]
Institute of Microbiology and Genetics [Göttingen]
Barton, Michael D [Auteur]
DOE Joint Genome Institute [Walnut Creek]
Lingner, Thomas [Auteur]
University Medical Center Göttingen [UMG]
Lin, Hsin-Hung [Auteur]
Institute of Population Health Sciences [Taiwan]
Liao, Yu-Chieh [Auteur]
Institute of Population Health Sciences [Taiwan]
Silva, Genivaldo Gueiros Z [Auteur]
San Diego State University [SDSU]
Cuevas, Daniel A [Auteur]
San Diego State University [SDSU]
Edwards, Robert A [Auteur]
San Diego State University [SDSU]
Saha, Surya [Auteur]
Boyce Thompson Institute [Ithaca]
Piro, Vitor C [Auteur]
Robert Koch Institute [Berlin] [RKI]
Ministry of Education [Brazil]
Renard, Bernhard y [Auteur]
Robert Koch Institute [Berlin] [RKI]
Pop, Mihai [Auteur]
Center for Bioinformatics and Computational Biology [Maryland] [CBCB]
Klenk, Hans-Peter [Auteur]
School of Biology [Newcastle upon Tyne]
Göker, Markus [Auteur]
Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures [DSMZ]
Kyrpides, Nikos C [Auteur]
DOE Joint Genome Institute [Walnut Creek]
biological sciences department [Jeddah]
Woyke, Tanja [Auteur]
DOE Joint Genome Institute [Walnut Creek]
Vorholt, Julia A [Auteur]
Institute of Microbiology [Zurich]
Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] [ETH Zürich]
Schulze-Lefert, Paul [Auteur]
Department of Plant Microbe Interactions
Cluster of Excellence on Plant Sciences [CEPLAS]
Rubin, Edward M [Auteur]
DOE Joint Genome Institute [Walnut Creek]
Darling, Aaron E [Auteur]
iThree Institute
Rattei, Thomas [Auteur]
Department of Microbiology and Ecosystem Science [Vienna]
Mchardy, Alice C [Auteur]
Algorithmische Bioinformatik [Düsseldorf]
Computational Biology of Infection Research [Braunschweig]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Cluster of Excellence on Plant Sciences [CEPLAS]

Journal title :

Nature Methods

Pages :

1063 - 1071

Publisher :

Nature Publishing Group

Publication date :

2017-10-02

ISSN :

1548-7091

HAL domain(s) :

Informatique [cs]/Bio-informatique [q-bio.QM]

English abstract : [en]

In metagenome analysis, computational methods for assembly, taxonomic profilingand binning are key components facilitating downstream biological datainterpretation. However, a lack of consensus about benchmarking datasets ...
Show more >In metagenome analysis, computational methods for assembly, taxonomic profilingand binning are key components facilitating downstream biological datainterpretation. However, a lack of consensus about benchmarking datasets andevaluation metrics complicates proper performance assessment. The CriticalAssessment of Metagenome Interpretation (CAMI) challenge has engaged the globaldeveloper community to benchmark their programs on datasets of unprecedentedcomplexity and realism. Benchmark metagenomes were generated from newlysequenced ~700 microorganisms and ~600 novel viruses and plasmids, includinggenomes with varying degrees of relatedness to each other and to publicly availableones and representing common experimental setups. Across all datasets, assemblyand genome binning programs performed well for species represented by individualgenomes, while performance was substantially affected by the presence of relatedstrains. Taxonomic profiling and binning programs were proficient at high taxonomicranks, with a notable performance decrease below the family level. Parametersettings substantially impacted performances, underscoring the importance ofprogram reproducibility. While highlighting current challenges in computationalmetagenomics, the CAMI results provide a roadmap for software selection to answerspecific research questions.Show less >

Language :

Anglais

Popular science :

Non

Collections :

• Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL