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Published, Version of Record (VoR)CC BY V4.0, Open
Journal article
Critical Assessment of Metagenome Interpretation: the second round of challenges
Nature methods, v 19(4), pp 429-440
Apr 2022
PMID: 35396482
Featured in Collection : UN Sustainable Development Goals @ Drexel
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.
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Details
- Title
- Critical Assessment of Metagenome Interpretation: the second round of challenges
- Creators
- Fernando Meyer - Helmholtz Centre for Infection ResearchAdrian Fritz - Helmholtz Centre for Infection ResearchZhi-Luo Deng - Helmholtz Centre for Infection ResearchDavid Koslicki - Pennsylvania State UniversityTill Robin Lesker - German Center for Infection ResearchAlexey Gurevich - St Petersburg UniversityGary Robertson - Helmholtz Centre for Infection ResearchMohammed Alser - ETH ZurichDmitry Antipov - St Petersburg UniversityFrancesco Beghini - University of TrentoDenis Bertrand - Genome Institute of SingaporeJaqueline J Brito - University of Southern CaliforniaC Titus Brown - University of California, DavisJan Buchmann - Heinrich Heine University DüsseldorfAydin Buluç - Lawrence Berkeley National LaboratoryBo Chen - Lawrence Berkeley National LaboratoryRayan Chikhi - Institut PasteurPhilip T L C Clausen - Technical University of DenmarkAlexandru Cristian - Drexel UniversityPiotr Wojciech Dabrowski - Hochschule für Technik und Wirtschaft Berlin, Berlin, GermanyAaron E Darling - University of Technology SydneyRob Egan - Joint Genome InstituteEleazar Eskin - University of California, Los AngelesEvangelos Georganas - IntelEugene Goltsman - Joint Genome InstituteMelissa A Gray - Drexel UniversityLars Hestbjerg Hansen - University of CopenhagenSteven Hofmeyr - Lawrence Berkeley National LaboratoryPingqin Huang - Fudan UniversityLuiz Irber - University of California, DavisHuijue Jia - BGI-Shenzhen, Shenzhen, China.Tue Sparholt Jørgensen - Novo Nordisk FoundationSilas D Kieser - University of GenevaTerje Klemetsen - UiT The Arctic University of NorwayAxel Kola - Charité - University Medicine BerlinMikhail Kolmogorov - Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.Anton Korobeynikov - St Petersburg UniversityJason Kwan - University of Wisconsin–MadisonNathan LaPierre - University of California, Los AngelesClaire Lemaitre - University of Rennes 1Chenhao Li - Genome Institute of SingaporeAntoine Limasset - University of LilleFabio Malcher-Miranda - Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, GermanySerghei Mangul - University of Southern CaliforniaVanessa R Marcelino - University of SydneyCamille Marchet - University of LillePierre Marijon - University of LilleDmitry Meleshko - St Petersburg UniversityDaniel R Mende - Amsterdam University Medical CentersAlessio Milanese - Swiss Institute of BioinformaticsNiranjan Nagarajan - Genome Institute of SingaporeJakob Nissen - DTU Health Tech, Kongens, Lyngby, Denmark.Sergey Nurk - National Human Genome Research InstituteLeonid Oliker - Lawrence Berkeley National LaboratoryLucas Paoli - Swiss Institute of BioinformaticsPierre Peterlongo - University of Rennes 1Vitor C Piro - Hasso Plattner InstituteJacob S Porter - University of VirginiaSimon Rasmussen - Novo Nordisk FoundationEvan R Rees - University of Wisconsin–MadisonKnut Reinert - Institute for Bioinformatics, FU Berlin, Berlin, Germany.Bernhard Renard - Hasso Plattner InstituteEspen Mikal Robertsen - UiT The Arctic University of NorwayGail L Rosen - Drexel UniversityHans-Joachim Ruscheweyh - Swiss Institute of BioinformaticsVaruni Sarwal - University of California, Los AngelesNicola Segata - University of TrentoEnrico Seiler - Institute for Bioinformatics, FU Berlin, Berlin, Germany.Lizhen Shi - Florida Polytechnic UniversityFengzhu Sun - University of Southern CaliforniaShinichi Sunagawa - Swiss Institute of BioinformaticsSøren Johannes Sørensen - University of CopenhagenAshleigh Thomas - Joint Genome InstituteChengxuan Tong - Genome Institute of SingaporeMirko Trajkovski - University of GenevaJulien Tremblay - National Research Council CanadaGherman Uritskiy - ID GenomicsRiccardo Vicedomini - Institut PasteurZhengyang Wang - Fudan UniversityZiye Wang - Fudan UniversityZhong Wang - Joint Genome InstituteAndrew Warren - University of VirginiaNils Peder Willassen - UiT The Arctic University of NorwayKatherine Yelick - Lawrence Berkeley National LaboratoryRonghui You - Fudan UniversityGeorg Zeller - Structural and Computational Biology Unit, EMBL, Heidelberg, Germany.Zhengqiao Zhao - Drexel UniversityShanfeng Zhu - Fudan UniversityJie Zhu - BGI-Shenzhen, Shenzhen, China.Ruben Garrido-Oter - Max Planck Institute for Plant Breeding ResearchPetra Gastmeier - Charité - University Medicine BerlinStephane Hacquard - Max Planck Institute for Plant Breeding ResearchSusanne Häußler - Helmholtz Centre for Infection Research, Braunschweig, GermanyAriane Khaledi - Helmholtz Centre for Infection ResearchFriederike Maechler - Charité - University Medicine BerlinFantin Mesny - Max Planck Institute for Plant Breeding ResearchSimona Radutoiu - Aarhus UniversityPaul Schulze-Lefert - Max Planck Institute for Plant Breeding ResearchNathiana Smit - Helmholtz Centre for Infection ResearchTill Strowig - Helmholtz Centre for Infection ResearchAndreas Bremges - Helmholtz Centre for Infection ResearchAlexander Sczyrba - Bielefeld UniversityAlice Carolyn McHardy - Helmholtz Centre for Infection Research
- Publication Details
- Nature methods, v 19(4), pp 429-440
- Publisher
- Springer Nature
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Electrical and Computer Engineering
- Web of Science ID
- WOS:000781199600010
- Scopus ID
- 2-s2.0-85127703163
- Other Identifier
- 991019168864704721
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- Industry collaboration
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Biochemical Research Methods