Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities

doi:10.1038/srep40371

QIBEBT-IR > 单细胞中心组群

	Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities
	Jing, Gongchao ; Sun, Zheng ; Wang, Honglei ; Gong, Yanhai ; Huang, Shi ; Ning, Kang ; Xu, Jian ; Su, Xiaoquan 1
	2017-01-12
发表期刊	SCIENTIFIC REPORTS
卷号	7
摘要	The number of metagenomes is increasing rapidly. However, current methods for metagenomic analysis are limited by their capability for in-depth data mining among a large number of microbiome each of which carries a complex community structure. Moreover, the complexity of configuring and operating computational pipeline also hinders efficient data processing for the end users. In this work we introduce Parallel-META 3, a comprehensive and fully automatic computational toolkit for rapid data mining among metagenomic datasets, with advanced features including 16S rRNA extraction for shotgun sequences, 16S rRNA copy number calibration, 16S rRNA based functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing. Application of Parallel-META 3 on 5,337 samples with 1,117,555,208 sequences from diverse studies and platforms showed it could produce similar results as QIIME and PICRUSt with much faster speed and lower memory usage, which demonstrates its ability to unravel the taxonomical and functional dynamics patterns across large datasets and elucidate ecological links between microbiome and the environment. Parallel-META 3 is implemented in C/C++ and R, and integrated into an executive package for rapid installation and easy access under Linux and Mac OS X. Both binary and source code packages are available at http://bioinfo.single-cell.cn/parallel-meta.html.
文章类型	Article
WOS标题词	Science & Technology
DOI	10.1038/srep40371
关键词[WOS]	GUT MICROBIOME ; DATABASE ; ARB
收录类别	SCI
语种	英语
WOS研究方向	Science & Technology - Other Topics
项目资助者	National Natural Science Foundation of China(61303161) ; Ministry of Science and Technology(2014AA21502) ; Open Fund of Key Laboratory of Marine Ecology and Environmental Science, Institute of Oceanology, Chinese Academy of Sciences(KLMEES201304) ; Soil Microbiome Program, Chinese Academy of Sciences(XDB15040100)
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000391669300001
引用统计
文献类型	期刊论文
条目标识符	http://ir.qibebt.ac.cn/handle/337004/9171
专题	单细胞中心组群
作者单位	1.Chinese Acad Sci, Single Cell Ctr, Shandong Key Lab Energy Genet, Qingdao 266101, Shandong, Peoples R China 2.Chinese Acad Sci, CAS Key Lab Biofuels, Qingdao Inst Bioenergy & Bioproc Technol, Qingdao 266101, Shandong, Peoples R China
推荐引用方式 GB/T 7714	Jing, Gongchao,Sun, Zheng,Wang, Honglei,et al. Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities[J]. SCIENTIFIC REPORTS,2017,7.
APA	Jing, Gongchao.,Sun, Zheng.,Wang, Honglei.,Gong, Yanhai.,Huang, Shi.,...&Su, Xiaoquan.(2017).Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities.SCIENTIFIC REPORTS,7.
MLA	Jing, Gongchao,et al."Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities".SCIENTIFIC REPORTS 7(2017).