Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities
文献类型：期刊论文
| 作者 | Jing, Gongchao; Sun, Zheng; Wang, Honglei; Gong, Yanhai; Huang, Shi; Ning, Kang; Xu, Jian; Su, Xiaoquan1 |
| 刊名 | SCIENTIFIC REPORTS
 |
| 出版日期 | 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 |
| 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). |
入库方式： OAI收割
来源：青岛生物能源与过程研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。