Journal
NATURE METHODS
Volume 19, Issue 4, Pages 429-+Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41592-022-01431-4
Keywords
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Funding
- DZIF [TI 12.002_00]
- German Excellence Cluster RESIST [EXC 2155, 390874280]
- NFDI4Microbiota [460129525]
- National Science Foundation [1664803, 1845890, 2041984, 1936791, 1919691]
- Saint Petersburg State University [PURE 73023672]
- Russian Science Foundation [19-14-00172]
- Gordon and Betty Moore Foundation's Data-Driven Discovery Initiative [GBMF4551]
- ANR Inception [ANR-16-CONV-0005]
- PRAIRIE [ANR-19-P3IA-0001]
- European Research Council (ERC) under the European Union
- Sydney Medical School Foundation
- ERC under the European Union
- Shanghai Municipal Science and Technology Commission [2018SHZDZX01]
- 111 Project [B18015]
- Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through the '2125 DECRyPT' Priority Program
- Department of Energy (DOE) Office of Biological and Environmental Research [DE-AC02-05CH11231]
- Swiss National Science Foundation (NCCR Microbiomes) [51NF40_180575]
- Office of Science of the US Department of Energy [DE-AC02-05CH11231]
- Swiss National Science Foundation (SNF) [51NF40_180575] Funding Source: Swiss National Science Foundation (SNF)
- Direct For Biological Sciences
- Div Of Biological Infrastructure [1845890, 2041984] Funding Source: National Science Foundation
- Direct For Computer & Info Scie & Enginr
- Office of Advanced Cyberinfrastructure (OAC) [1919691] Funding Source: National Science Foundation
- Direct For Mathematical & Physical Scien
- Division Of Mathematical Sciences [1664803] Funding Source: National Science Foundation
- Div Of Biological Infrastructure
- Direct For Biological Sciences [1936791] Funding Source: National Science Foundation
- Agence Nationale de la Recherche (ANR) [ANR-16-CONV-0005] Funding Source: Agence Nationale de la Recherche (ANR)
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This study presents the results of the second round of the Critical Assessment of Metagenome Interpretation challenges (CAMI II), which is a community-driven effort for comprehensively benchmarking tools for metagenomics data analysis. The results show substantial improvements in assembly, but related strains and assembly quality still pose challenges. Taxon profilers and binners excel at higher bacterial ranks but underperform for viruses and Archaea. The need to improve reproducibility is emphasized by the clinical pathogen detection results.
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. This study presents the results of the second round of the Critical Assessment of Metagenome Interpretation challenges (CAMI II), which is a community-driven effort for comprehensively benchmarking tools for metagenomics data analysis.
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