gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data

Abstract Meta-omics approaches have been increasingly used to study the structure and function of the microbial communities. A variety of large-scale collaborative projects are being conducted to encompass samples from diverse environments and habitats. This change has resulted in enormous demands f...

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Bibliographic Details
Published in:Nucleic acids research 2019-01, Vol.47 (D1), p.D637-D648
Main Authors: Shi, Wenyu, Qi, Heyuan, Sun, Qinglan, Fan, Guomei, Liu, Shuangjiang, Wang, Jun, Zhu, Baoli, Liu, Hongwei, Zhao, Fangqing, Wang, Xiaochen, Hu, Xiaoxuan, Li, Wei, Liu, Jia, Tian, Ye, Wu, Linhuan, Ma, Juncai
Format: Article
Language:English
Subjects:
Database Issue
Databases, Genetic
Metagenome
Metagenomics - methods
Metagenomics - standards
Microbiota
Reference Standards
Software
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Summary:Abstract Meta-omics approaches have been increasingly used to study the structure and function of the microbial communities. A variety of large-scale collaborative projects are being conducted to encompass samples from diverse environments and habitats. This change has resulted in enormous demands for long-term data maintenance and capacity for data analysis. The Global Catalogue of Metagenomics (gcMeta) is a part of the ‘Chinese Academy of Sciences Initiative of Microbiome (CAS-CMI)’, which focuses on studying the human and environmental microbiome, establishing depositories of samples, strains and data, as well as promoting international collaboration. To accommodate and rationally organize massive datasets derived from several thousands of human and environmental microbiome samples, gcMeta features a database management system for archiving and publishing data in a standardized way. Another main feature is the integration of more than ninety web-based data analysis tools and workflows through a Docker platform which enables data analysis by using various operating systems. This platform has been rapidly expanding, and now hosts data from the CAS-CMI and a number of other ongoing research projects. In conclusion, this platform presents a powerful and user-friendly service to support worldwide collaborative efforts in the field of meta-omics research. This platform is freely accessible at https://gcmeta.wdcm.org/.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gky1008