Title :

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

Author(s) :

Sczyrba, Alexander [Auteur correspondant]
Center for Biotechnology [CeBiTec]
Hofmann, Peter [Auteur]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Algorithmische Bioinformatik [Düsseldorf]
Belmann, Peter [Auteur]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Center for Biotechnology [CeBiTec]
Koslicki, David [Auteur]
Department of Mathematics [Corvallis, Oregon]
Janssen, Stefan [Auteur]

Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Dröge, Johannes [Auteur]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Algorithmische Bioinformatik [Düsseldorf]
Gregor, Ivan [Auteur]
Max Planck Institute for Informatics [Saarbrücken]
Algorithmische Bioinformatik [Düsseldorf]
Majda, Stephan [Auteur]
Faculty of Biology [Essen]
Algorithmische Bioinformatik [Düsseldorf]
Fiedler, Jessika [Auteur]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Algorithmische Bioinformatik [Düsseldorf]
Dahms, Eik [Auteur]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Algorithmische Bioinformatik [Düsseldorf]
Bremges, Andreas [Auteur]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
German Center for Infection Research - partner site Hannover-Braunschweig [DZIF]
Center for Biotechnology [CeBiTec]
Fritz, Adrian [Auteur]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Garrido-Oter, Ruben [Auteur]
Cluster of Excellence on Plant Sciences [CEPLAS]
Department of Plant Microbe Interactions
Algorithmische Bioinformatik [Düsseldorf]
Jørgensen, Tue Sparholt [Auteur]
Section of Microbiology [Copenhagen]
Department of Environmental Science [Roskilde] [ENVS]
Shapiro, Nicole [Auteur]
DOE Joint Genome Institute [Walnut Creek]
Blood, Philip D [Auteur]
Pittsburgh Supercomputing Center [PSC]
Gurevich, Alexey [Auteur]
Bai, Yang [Auteur]
Centre of Excellence for Plant and Microbial Sciences [CEPAMS]
Department of Plant Microbe Interactions
Turaev, Dmitrij [Auteur]
Demaere, Matthew Z [Auteur]
iThree Institute
Chikhi, Rayan [Auteur]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Bioinformatics and Sequence Analysis [BONSAI]
Nagarajan, Niranjan [Auteur]
Quince, Christopher [Auteur]
Hansen, Lars Hestbjerg [Auteur]
Department of Environmental Science [Roskilde] [ENVS]
Sørensen, Søren J [Auteur]
Section of Microbiology [Copenhagen]
Chia, Burton K H [Auteur]
Denis, Bertrand [Auteur]
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]
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]
Graduate Institute of Biomedical Informatics [Taipei]
Joint BioEnergy Institute [Emeryville]
Singer, Steven W [Auteur]
Biological Systems and Engineering [LBNL Berkeley]
Joint BioEnergy Institute [Emeryville]
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]
Ministry of Education [Brazil]
Robert Koch Institute [Berlin] [RKI]
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]
Woyke, Tanja [Auteur]
DOE Joint Genome Institute [Walnut Creek]
Vorholt, Julia A [Auteur]
Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] [ETH Zürich]
Institute of Microbiology [Zurich]
Schulze-Lefert, Paul [Auteur]
Cluster of Excellence on Plant Sciences [CEPLAS]
Department of Plant Microbe Interactions
Rubin, Edward M [Auteur]
DOE Joint Genome Institute [Walnut Creek]
Darling, Aaron E [Auteur]
iThree Institute
Rattei, Thomas [Auteur]
Mchardy, Alice C [Auteur]
Cluster of Excellence on Plant Sciences [CEPLAS]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Algorithmische Bioinformatik [Düsseldorf]

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

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

Collections :

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

Source :

Harvested from HAL