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

CORC > 青岛生物能源与过程研究所 > 中国科学院青岛生物能源与过程研究所 > 单细胞中心

	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
刊名	SCIENTIFIC REPORTS
	2017-01-12
卷号	7
英文摘要	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.
WOS标题词	Science & Technology
类目[WOS]	Multidisciplinary Sciences
研究领域[WOS]	Science & Technology - Other Topics
关键词[WOS]	GUT MICROBIOME ; DATABASE ; ARB
收录类别	SCI
语种	英语
WOS记录号	WOS:000391669300001
内容类型	期刊论文
源URL	[http://ir.qibebt.ac.cn/handle/337004/9171]
专题	青岛生物能源与过程研究所_单细胞中心
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).