Title :

Critical Assessment of Metagenome Interpretation: the second round of challenges

Author(s) :

Meyer, Fernando [Auteur]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Fritz, Adrian [Auteur]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Deng, Zhi-Luo [Auteur]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Koslicki, David [Auteur]
Pennsylvania State University [Penn State]
Lesker, Till Robin [Auteur]
German Center for Infection Research - partner site Hannover-Braunschweig [DZIF]
Gurevich, Alexey [Auteur]
Saint Petersburg State University [SPBU]
Robertson, Gary [Auteur]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Alser, Mohammed [Auteur]
Antipov, Dmitry [Auteur]
Beghini, Francesco [Auteur]
Centre for Integrative Biology (CIBIO), University of Trento [CIBIO]
Bertrand, Denis [Auteur]
Genome Institute of Singapore [GIS]
Brito, Jaqueline [Auteur]
University of Southern California [USC]
Brown, C. Titus [Auteur]
University of California [Davis] [UC Davis]
Buchmann, Jan [Auteur]
Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]
Buluç, Aydin [Auteur]
Lawrence Berkeley National Laboratory [Berkeley] [LBNL]
Chen, Bo [Auteur]
Lawrence Berkeley National Laboratory [Berkeley] [LBNL]
Chikhi, Rayan [Auteur]
Institut Pasteur [Paris] [IP]
Clausen, Philip [Auteur]
National Food Institute [Lyngby] [Forside]
Cristian, Alexandru [Auteur]
Drexel University
Dabrowski, Piotr Wojciech [Auteur]
Robert Koch Institute [Berlin] [RKI]
Darling, Aaron [Auteur]
University of Technology Sydney [UTS]
Egan, Rob [Auteur]
DOE Joint Genome Institute [Walnut Creek]
Eskin, Eleazar [Auteur]
University of California [Los Angeles] [UCLA]
Georganas, Evangelos [Auteur]
Intel Corporation [Santa Clara]
Goltsman, Eugene [Auteur]
DOE Joint Genome Institute [Walnut Creek]
Gray, Melissa [Auteur]
Drexel University
Hansen, Lars Hestbjerg [Auteur]
Department of Plant and Environmental Sciences [Frederiksberg]
Hofmeyr, Steven [Auteur]
Lawrence Berkeley National Laboratory [Berkeley] [LBNL]
Huang, Pingqin [Auteur]
Fudan University [Shanghai]
Irber, Luiz [Auteur]
University of California [Davis] [UC Davis]
Jia, Huijue [Auteur]
Beijing Genomics Institute [Shenzhen] [BGI]
Jørgensen, Tue Sparholt [Auteur]
Kieser, Silas [Auteur]
Université de Genève = University of Geneva [UNIGE]
Klemetsen, Terje [Auteur]
The Arctic University of Norway [Tromsø, Norway] [UiT]
Kola, Axel [Auteur]
Charité - UniversitätsMedizin = Charité - University Hospital [Berlin]
Kolmogorov, Mikhail [Auteur]
University of California [San Diego] [UC San Diego]
Korobeynikov, Anton [Auteur]
Saint Petersburg State University [SPBU]
Kwan, Jason [Auteur]
University of Wisconsin-Madison
Lapierre, Nathan [Auteur]
University of California [Los Angeles] [UCLA]
Lemaitre, Claire [Auteur]
Scalable, Optimized and Parallel Algorithms for Genomics [GenScale]
Li, Chenhao [Auteur]
Genome Institute of Singapore [GIS]
Limasset, Antoine [Auteur]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Malcher-Miranda, Fabio [Auteur]
Hasso Plattner Institute [Potsdam, Germany]
Mangul, Serghei [Auteur]
University of Southern California [USC]
Marcelino, Vanessa [Auteur]
The University of Sydney
Marchet, Camille [Auteur]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Marijon, Pierre [Auteur]
Inria Lille - Nord Europe
Meleshko, Dmitry [Auteur]
Mende, Daniel [Auteur]
Amsterdam UMC - Amsterdam University Medical Center
Milanese, Alessio [Auteur]
Structural and Computational Biology
Nagarajan, Niranjan [Auteur]
Genome Institute of Singapore [GIS]
Nissen, Jakob [Auteur]
DTU Electrical Engineering [Lyngby]
Nurk, Sergey [Auteur]
Oliker, Leonid [Auteur]
Lawrence Berkeley National Laboratory [Berkeley] [LBNL]
Paoli, Lucas [Auteur]
Piro, Vitor [Auteur]
Hasso Plattner Institute [Potsdam, Germany]
Porter, Jacob [Auteur]
University of Virginia
Rasmussen, Simon [Auteur]
IT University of Copenhagen [ITU]
Rees, Evan [Auteur]
University of Wisconsin-Madison
Reinert, Knut [Auteur]
Freie Universität Berlin
Renard, Bernhard [Auteur]
University of Potsdam = Universität Potsdam
Robertsen, Espen Mikal [Auteur]
The Arctic University of Norway [Tromsø, Norway] [UiT]
Rosen, Gail [Auteur]
Drexel University
Ruscheweyh, Hans-Joachim [Auteur]
Sarwal, Varuni [Auteur]
University of California [Los Angeles] [UCLA]
Segata, Nicola [Auteur]
Centre for Integrative Biology (CIBIO), University of Trento [CIBIO]
Seiler, Enrico [Auteur]
Freie Universität Berlin
Shi, Lizhen [Auteur]
Florida International University [Miami] [FIU]
Sun, Fengzhu [Auteur]
University of Southern California [USC]
Sunagawa, Shinichi [Auteur]
Freie Universität Berlin
Sørensen, Søren Johannes [Auteur]
IT University of Copenhagen [ITU]
Thomas, Ashleigh [Auteur]
DOE Joint Genome Institute [Walnut Creek]
Tong, Chengxuan [Auteur]
Genome Institute of Singapore [GIS]
Trajkovski, Mirko [Auteur]
Université de Genève = University of Geneva [UNIGE]
Tremblay, Julien [Auteur]
National Research Council of Canada [NRC]
Uritskiy, Gherman [Auteur]
Phase Genomics [Seattle]
Vicedomini, Riccardo [Auteur]
Institut Pasteur [Paris] [IP]
Wang, Zhengyang [Auteur]
Fudan University [Shanghai]
Wang, Ziye [Auteur]
Fudan University [Shanghai]
Wang, Zhong [Auteur]
Lawrence Berkeley National Laboratory [Berkeley] [LBNL]
Warren, Andrew [Auteur]
University of Virginia
Willassen, Nils Peder [Auteur]
The Arctic University of Norway [Tromsø, Norway] [UiT]
Yelick, Katherine [Auteur]
Lawrence Berkeley National Laboratory [Berkeley] [LBNL]
You, Ronghui [Auteur]
Fudan University [Shanghai]
Zeller, Georg [Auteur]
Structural and Computational Biology
Zhao, Zhengqiao [Auteur]
Drexel University
Zhu, Shanfeng [Auteur]
Fudan University [Shanghai]
Zhu, Jie [Auteur]
Beijing Genomics Institute [Shenzhen] [BGI]
Garrido-Oter, Ruben [Auteur]
Max Planck Institute for Plant Breeding Research [MPIPZ]
Gastmeier, Petra [Auteur]
Charité - UniversitätsMedizin = Charité - University Hospital [Berlin]
Hacquard, Stephane [Auteur]
Max Planck Institute for Plant Breeding Research [MPIPZ]
Häußler, Susanne [Auteur]
Helmholtz Centre for Infection Research [HZI]
Khaledi, Ariane [Auteur]
Helmholtz Centre for Infection Research [HZI]
Maechler, Friederike [Auteur]
Charité - UniversitätsMedizin = Charité - University Hospital [Berlin]
Mesny, Fantin [Auteur]
Max Planck Institute for Plant Breeding Research [MPIPZ]
Radutoiu, Simona [Auteur]
Aarhus University [Aarhus]
Schulze-Lefert, Paul [Auteur]
Max Planck Institute for Plant Breeding Research [MPIPZ]
Smit, Nathiana [Auteur]
Helmholtz Centre for Infection Research [HZI]
Strowig, Till [Auteur]
Helmholtz Centre for Infection Research [HZI]
Bremges, Andreas [Auteur]
Helmholtz Centre for Infection Research [HZI]
Sczyrba, Alexander [Auteur]
Center for Biotechnology [CeBiTec]
Mchardy, Alice Carolyn [Auteur]
Braunschweig Integrated Centre of Systems Biology [Braunschweig] [BRICS]
Peterlongo, Pierre [Auteur]
Scalable, Optimized and Parallel Algorithms for Genomics [GenScale]

Journal title :

Nature Methods

Pages :

429-440

Publisher :

Nature Publishing Group

Publication date :

2022-04

ISSN :

1548-7091

HAL domain(s) :

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

English abstract : [en]

Abstract Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community ...
Show more >Abstract Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.Show less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

ANR Project :

Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs
PaRis Artificial Intelligence Research InstitutE

Collections :

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

Source :

Harvested from HAL