Benchmarking Metagenomics Tools for Taxonomic Classification

被引：319

作者：

Ye, Simon H. ^{[1
,2
]}

Siddle, Katherine J. ^{[2
,3
]}

Park, Daniel J. ^{[2
]}

Sabeti, Pardis C. ^{[2
,3
,4
,5
]}

机构：

[1] MIT, Harvard Hlth Sci & Technol, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[2] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA

[3] Harvard Univ, Dept Organismal & Evolutionary Biol, Ctr Syst Biol, Cambridge, MA 02138 USA

[4] Harvard Sch Publ Hlth, Dept Immunol & Infect Dis, Boston, MA 02115 USA

[5] HHMI, Chevy Chase, MD 20815 USA

来源：

CELL | 2019年 / 178卷 / 04期

关键词：

ALIGNMENT; SURVEILLANCE; SEQUENCES; ABUNDANCE;

D O I：

10.1016/j.cell.2019.07.010

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform taxonomic classification of these data. The fast pace of development of these tools and the complexity of metagenomic data make it important that researchers are able to benchmark their performance. Here, we review current approaches for metagenomic analysis and evaluate the performance of 20 metagenomic classifiers using simulated and experimental datasets. We describe the key metrics used to assess performance, offer a framework for the comparison of additional classifiers, and discuss the future of metagenomic data analysis.

引用

页码：779 / 794

页数：16

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