Critical Assessment of Metagenome Interpretation: the second round of challenges.

Autor: Meyer F; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany., Fritz A; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.; German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany., Deng ZL; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany., Koslicki D; Pennsylvania State University, State College, PA, USA., Lesker TR; German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany.; Helmholtz Centre for Infection Research, Braunschweig, Germany., Gurevich A; Saint Petersburg State University, Saint Petersburg, Russia., Robertson G; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany., Alser M; Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland., Antipov D; Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia., Beghini F; Department CIBIO, University of Trento, Trento, Italy., Bertrand D; Genome Institute of Singapore, Singapore, Singapore., Brito JJ; University of Southern California, Los Angeles, CA, USA., Brown CT; University of California, Davis, Davis, CA, USA., Buchmann J; Institute for Biological Data Science, Heinrich-Heine-University, Düsseldorf, Germany., Buluç A; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; University of California, Berkeley, Berkeley, CA, USA., Chen B; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; University of California, Berkeley, Berkeley, CA, USA., Chikhi R; Institut Pasteur, Paris, France., Clausen PTLC; National Food Institute, Division of Global Surveillance, Technical University of Denmark, Lyngby, Denmark., Cristian A; Drexel University, Philadelphia, PA, USA.; Google Inc., Philadelphia, PA, USA., Dabrowski PW; Robert Koch-Institut, Berlin, Germany.; Hochschule für Technik und Wirtschaft Berlin, Berlin, Germany., Darling AE; University of Technology Sydney, Sydney, Australia., Egan R; DOE Joint Genome Institute, Berkeley, CA, USA.; Lawrence Berkeley National Laboratories, Berkeley, CA, USA., Eskin E; University of California, Los Angeles, Los Angeles, CA, USA., Georganas E; Intel Corporation, Santa Clara, CA, USA., Goltsman E; DOE Joint Genome Institute, Berkeley, CA, USA.; Lawrence Berkeley National Laboratories, Berkeley, CA, USA., Gray MA; Drexel University, Philadelphia, PA, USA.; Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Philadelphia, PA, USA., Hansen LH; University of Copenhagen, Department of Plant and Environmental Science, Frederiksberg, Denmark., Hofmeyr S; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; University of California, Berkeley, Berkeley, CA, USA., Huang P; School of Computer Science, Fudan University, Shanghai, China., Irber L; University of California, Davis, Davis, CA, USA., Jia H; BGI-Shenzhen, Shenzhen, China.; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China., Jørgensen TS; Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Lyngby, Denmark.; Aarhus University, Department of Environmental Science, Roskilde, Denmark., Kieser SD; Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.; Swiss Institute of Bioinformatics, Geneva, Switzerland., Klemetsen T; The Arctic University of Norway, Tromsø, Norway., Kola A; Charité-Universitätsmedizin Berlin, Berlin, Germany., Kolmogorov M; Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA., Korobeynikov A; Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.; Department of Statistical Modelling, Saint Petersburg State University, Saint Petersburg, Russia., Kwan J; University of Wisconsin-Madison, Madison, WI, USA., LaPierre N; University of California, Los Angeles, Los Angeles, CA, USA., Lemaitre C; Univ. Rennes, Inria, CNRS, IRISA, Rennes, France., Li C; Genome Institute of Singapore, Singapore, Singapore., Limasset A; Université Lille, CNRS, CRIStAL, Lille, France., Malcher-Miranda F; Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany., Mangul S; University of Southern California, Los Angeles, CA, USA., Marcelino VR; Sydney Medical School, The University of Sydney, Sydney, Australia.; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia., Marchet C; Université Lille, CNRS, CRIStAL, Lille, France., Marijon P; Department of Computer Science, Inria, University of Lille, CNRS, Lille, France., Meleshko D; Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia., Mende DR; Amsterdam University Medical Center, Amsterdam, the Netherlands., Milanese A; Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany., Nagarajan N; Genome Institute of Singapore, A*STAR, Singapore, Singapore.; National University of Singapore, Singapore, Singapore., Nissen J; DTU Health Tech, Kongens, Lyngby, Denmark., Nurk S; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA., Oliker L; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; University of California, Berkeley, Berkeley, CA, USA., Paoli L; Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland., Peterlongo P; Univ. Rennes, Inria, CNRS, IRISA, Rennes, France., Piro VC; Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany., Porter JS; University of Virginia, Charlottesville, VA, USA., Rasmussen S; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark., Rees ER; University of Wisconsin-Madison, Madison, WI, USA., Reinert K; Institute for Bioinformatics, FU Berlin, Berlin, Germany., Renard B; Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany.; Bioinformatics Unit (MF1), Robert Koch Institute, Berlin, Germany., Robertsen EM; The Arctic University of Norway, Tromsø, Norway., Rosen GL; Drexel University, Philadelphia, PA, USA.; Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Philadelphia, PA, USA.; Center for Biological Discovery from Big Data, Philadelphia, PA, USA., Ruscheweyh HJ; Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland., Sarwal V; University of California, Los Angeles, Los Angeles, CA, USA., Segata N; Department CIBIO, University of Trento, Trento, Italy., Seiler E; Institute for Bioinformatics, FU Berlin, Berlin, Germany., Shi L; Florida Polytechnic University, Lakeland, FL, USA., Sun F; Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA, USA., Sunagawa S; Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland., Sørensen SJ; University of Copenhagen, Copenhagen, Denmark., Thomas A; DOE Joint Genome Institute, Berkeley, CA, USA.; University of British Columbia, Vancouver, British Columbia, Canada., Tong C; Genome Institute of Singapore, Singapore, Singapore., Trajkovski M; Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.; Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland., Tremblay J; Energy, Mining and Environment, National Research Council Canada, Montreal, Quebec, Canada., Uritskiy G; Phase Genomics, Seattle, WA, USA., Vicedomini R; Institut Pasteur, Paris, France., Wang Z; School of Computer Science, Fudan University, Shanghai, China., Wang Z; School of Mathematical Sciences, Fudan University, Shanghai, China., Wang Z; Department of Energy Joint Genome Institute, Berkeley, CA, USA.; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; School of Natural Sciences, University of California at Merced, Merced, CA, USA., Warren A; University of Virginia, Charlottesville, VA, USA., Willassen NP; The Arctic University of Norway, Tromsø, Norway., Yelick K; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; University of California, Berkeley, Berkeley, CA, USA., You R; School of Computer Science, Fudan University, Shanghai, China., Zeller G; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany., Zhao Z; Drexel University, Philadelphia, PA, USA., Zhu S; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China., Zhu J; BGI-Shenzhen, Shenzhen, China.; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China., Garrido-Oter R; Max Planck Institute for Plant Breeding Research, Köln, Germany., Gastmeier P; Charité-Universitätsmedizin Berlin, Berlin, Germany., Hacquard S; Max Planck Institute for Plant Breeding Research, Köln, Germany., Häußler S; Helmholtz Centre for Infection Research, Braunschweig, Germany., Khaledi A; Helmholtz Centre for Infection Research, Braunschweig, Germany., Maechler F; Charité-Universitätsmedizin Berlin, Berlin, Germany., Mesny F; Max Planck Institute for Plant Breeding Research, Köln, Germany., Radutoiu S; Aarhus University, Aarhus, Denmark., Schulze-Lefert P; Max Planck Institute for Plant Breeding Research, Köln, Germany., Smit N; Helmholtz Centre for Infection Research, Braunschweig, Germany., Strowig T; Helmholtz Centre for Infection Research, Braunschweig, Germany., Bremges A; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.; German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany., Sczyrba A; Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany., McHardy AC; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany. amc14@helmholtz-hzi.de.; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany. amc14@helmholtz-hzi.de.; German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany. amc14@helmholtz-hzi.de.; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany. amc14@helmholtz-hzi.de.
Jazyk: angličtina
Zdroj: Nature methods [Nat Methods] 2022 Apr; Vol. 19 (4), pp. 429-440. Date of Electronic Publication: 2022 Apr 08.
DOI: 10.1038/s41592-022-01431-4
Abstrakt: 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.
(© 2022. The Author(s).)
Databáze: MEDLINE
Externí odkaz: