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Assessment of quality control approaches for metagenomic data analysis
Zhou, Qian; Su, Xiaoquan; Ning, Kang1
2014-11-07
发表期刊SCIENTIFIC REPORTS
卷号4期号:1页码:1
摘要

Currently there is an explosive increase of the next-generation sequencing (NGS) projects and related datasets, which have to be processed by Quality Control (QC) procedures before they could be utilized for omics analysis. QC procedure usually includes identification and filtration of sequencing artifacts such as low-quality reads and contaminating reads, which would significantly affect and sometimes mislead downstream analysis. Quality control of NGS data for microbial communities is especially challenging. In this work, we have evaluated and compared the performance and effects of various QC pipelines on different types of metagenomic NGS data and from different angles, based on which general principles of using QC pipelines were proposed. Results based on both simulated and real metagenomic datasets have shown that: firstly, QC-Chain is superior in its ability for contamination identification for metagenomic NGS datasets with different complexities with high sensitivity and specificity. Secondly, the high performance computing engine enabled QC-Chain to achieve a significant reduction in processing time compared to other pipelines based on serial computing. Thirdly, QC-Chain could outperform other tools in benefiting downstream metagenomic data analysis.

文章类型Article
WOS标题词Science & Technology
DOI10.1038/srep06957
收录类别SCI
语种英语
WOS研究方向Science & Technology - Other Topics
WOS类目Multidisciplinary Sciences
WOS记录号WOS:000344385100009
引用统计
文献类型期刊论文
条目标识符http://ir.qibebt.ac.cn/handle/337004/6366
专题单细胞中心组群
作者单位1.Chinese Acad Sci, Shandong Key Lab Energy Genet, Bioinformat Grp Single Cell Ctr, Qingdao 266101, Shandong, Peoples R China
2.Chinese Acad Sci, Qingdao Inst Bioenergy & Bioproc Technol, CAS Key Lab Biofuels, Qingdao 266101, Shandong, Peoples R China
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Zhou, Qian,Su, Xiaoquan,Ning, Kang. Assessment of quality control approaches for metagenomic data analysis[J]. SCIENTIFIC REPORTS,2014,4(1):1.
APA Zhou, Qian,Su, Xiaoquan,&Ning, Kang.(2014).Assessment of quality control approaches for metagenomic data analysis.SCIENTIFIC REPORTS,4(1),1.
MLA Zhou, Qian,et al."Assessment of quality control approaches for metagenomic data analysis".SCIENTIFIC REPORTS 4.1(2014):1.
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