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Critical Assessment of Metagenome Interpretation: the second round of challenges
Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review
Dokumenter
- s41592-022-01431-4
Forlagets udgivne version, 4 MB, PDF-dokument
DOI
- https://doi.org/10.1038/s41592-022-01431-4
Forlagets udgivne version
- Fernando Meyer, Helmholtz Centre for Infection Research, Technical University of Braunschweig ,
- Adrian Fritz, Helmholtz Centre for Infection Research, Technical University of Braunschweig ,
- Zhi Luo Deng, Helmholtz Centre for Infection Research, Technical University of Braunschweig, Hannover Medical School ,
- David Koslicki, Pennsylvania State University ,
- Till Robin Lesker, Helmholtz Centre for Infection Research ,
- Alexey Gurevich, St. Petersburg State University ,
- Gary Robertson, Helmholtz Centre for Infection Research, Technical University of Braunschweig ,
- Mohammed Alser, ETH Zürich ,
- Dmitry Antipov, St. Petersburg State University ,
- Francesco Beghini, University of Trento ,
- Denis Bertrand, Agency for Science, Technology and Research ,
- Jaqueline J. Brito, University of Southern California ,
- C. Titus Brown, University of California at Davis ,
- Jan Buchmann, Heinrich Heine University Düsseldorf ,
- Aydin Buluç, Lawrence Berkeley National Laboratory, University of California at Berkeley ,
- Bo Chen, Lawrence Berkeley National Laboratory, University of California at Berkeley ,
- Rayan Chikhi, Institut Pasteur Paris ,
- Philip T.L.C. Clausen, Danmarks Tekniske Universitet ,
- Alexandru Cristian, Drexel University, Alphabet Inc. ,
- Piotr Wojciech Dabrowski, Robert Koch-Institut, University of Applied Sciences Berlin ,
- Aaron E. Darling, University of Technology Sydney ,
- Rob Egan, United States Department of Energy, Lawrence Berkeley National Laboratory ,
- Eleazar Eskin, University of California at Los Angeles ,
- Evangelos Georganas, Intel ,
- Eugene Goltsman, United States Department of Energy, Lawrence Berkeley National Laboratory ,
- Melissa A. Gray, Drexel University, Ecological and Evolutionary Signal-Processing and Informatics Laboratory ,
- Lars Hestbjerg Hansen, Københavns Universitet ,
- Steven Hofmeyr, Lawrence Berkeley National Laboratory, University of California at Berkeley ,
- Pingqin Huang, Fudan University ,
- Luiz Irber, University of California at Davis ,
- Huijue Jia, BGI-Shenzhen ,
- Tue Sparholt Jørgensen, Danmarks Tekniske Universitet ,
- Silas D. Kieser, University of Geneva, Swiss Institute of Bioinformatics ,
- Terje Klemetsen, UiT The Arctic University of Norway ,
- Axel Kola, Charité-Universitätsmedizin Berlin ,
- Mikhail Kolmogorov, Department of Computer Science and Engineering ,
- Anton Korobeynikov, St. Petersburg State University ,
- Jason Kwan, University of Wisconsin-Madison ,
- Nathan LaPierre, University of California at Los Angeles ,
- Claire Lemaitre, CNRS ,
- Chenhao Li, Agency for Science, Technology and Research ,
- Antoine Limasset, Université de Lille ,
- Fabio Malcher-Miranda, University of Potsdam ,
- Serghei Mangul, University of Southern California ,
- Vanessa R. Marcelino, University of Sydney, Hudson Institute of Medical Research ,
- Camille Marchet, Université de Lille ,
- Pierre Marijon, Université de Lille ,
- Dmitry Meleshko, St. Petersburg State University ,
- Daniel R. Mende, University of Amsterdam ,
- Alessio Milanese, ETH Zürich, European Molecular Biology Laboratory ,
- Niranjan Nagarajan, Agency for Science, Technology and Research, National University of Singapore ,
- Jakob Nissen, Danmarks Tekniske Universitet ,
- Sergey Nurk, National Institutes of Health ,
- Leonid Oliker, Lawrence Berkeley National Laboratory, University of California at Berkeley ,
- Lucas Paoli, ETH Zürich ,
- Pierre Peterlongo, CNRS ,
- Vitor C. Piro, University of Potsdam ,
- Jacob S. Porter, University of Virginia ,
- Simon Rasmussen, Københavns Universitet ,
- Evan R. Rees, University of Wisconsin-Madison ,
- Knut Reinert, Free University of Berlin ,
- Bernhard Renard, University of Potsdam, Robert Koch-Institut ,
- Espen Mikal Robertsen, UiT The Arctic University of Norway ,
- Gail L. Rosen, Drexel University, Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Center for Biological Discovery from Big Data ,
- Hans Joachim Ruscheweyh, ETH Zürich ,
- Varuni Sarwal, University of California at Los Angeles ,
- Nicola Segata, University of Trento ,
- Enrico Seiler, Free University of Berlin ,
- Lizhen Shi, Florida Polytechnic University ,
- Fengzhu Sun, University of Southern California ,
- Shinichi Sunagawa, ETH Zürich ,
- Søren Johannes Sørensen, Københavns Universitet ,
- Ashleigh Thomas, United States Department of Energy, University of British Columbia ,
- Chengxuan Tong, Agency for Science, Technology and Research ,
- Mirko Trajkovski, University of Geneva ,
- Julien Tremblay, National Research Council of Canada ,
- Gherman Uritskiy, Phase Genomics ,
- Riccardo Vicedomini, Institut Pasteur Paris ,
- Zhengyang Wang, Fudan University ,
- Ziye Wang, Fudan University ,
- Zhong Wang, United States Department of Energy, Lawrence Berkeley National Laboratory, University of California Merced ,
- Andrew Warren, University of Virginia ,
- Nils Peder Willassen, UiT The Arctic University of Norway ,
- Katherine Yelick, Lawrence Berkeley National Laboratory, University of California at Berkeley ,
- Ronghui You, Fudan University ,
- Georg Zeller, European Molecular Biology Laboratory ,
- Zhengqiao Zhao, Drexel University ,
- Shanfeng Zhu, Fudan University ,
- Jie Zhu, BGI-Shenzhen ,
- Ruben Garrido-Oter, Max Planck Institute for Plant Breeding Research ,
- Petra Gastmeier, Charité-Universitätsmedizin Berlin ,
- Stephane Hacquard, Max Planck Institute for Plant Breeding Research ,
- Susanne Häußler, Helmholtz Centre for Infection Research ,
- Ariane Khaledi, Helmholtz Centre for Infection Research ,
- Friederike Maechler, Charité-Universitätsmedizin Berlin ,
- Fantin Mesny, Max Planck Institute for Plant Breeding Research ,
- Simona Radutoiu
- Paul Schulze-Lefert, Max Planck Institute for Plant Breeding Research ,
- Nathiana Smit, Helmholtz Centre for Infection Research ,
- Till Strowig, Helmholtz Centre for Infection Research ,
- Andreas Bremges, Helmholtz Centre for Infection Research ,
- Alexander Sczyrba, Bielefeld University ,
- Alice Carolyn McHardy, Helmholtz Centre for Infection Research, Technical University of Braunschweig, Hannover Medical School
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.
| Originalsprog | Engelsk |
|---|---|
| Tidsskrift | Nature Methods |
| Vol/bind | 19 |
| Nummer | 4 |
| Sider (fra-til) | 429-440 |
| Antal sider | 12 |
| ISSN | 1548-7091 |
| DOI | |
| Status | Udgivet - apr. 2022 |
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