引用程序和文献

微生物多样性分析模块,均源于该领域公开发表文献中,广受认可的算法和开源程序。

详细信息,参考软件内置模块帮助文档,或点击在线帮助文档,进行查看。

简介如下所示:


1、原始数据质控

Trimmomatic v0.32 ( http://www.usadellab.org/cms/index.php?page=trimmomatic )

Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170.


2、PE数据组装

FLASH v1.2.11(https://ccb.jhu.edu/software/FLASH/)

FLASH: Fast length adjustment of short reads to improve genome assemblies. T. Magoc and S. Salzberg. Bioinformatics 27:21 (2011), 2957-63.


3、样本OTU聚类和丰度信息计算

Usearch v8.1.1861(http://www.drive5.com/usearch/manual/)

USEARCH and UCLUST algorithms:Edgar,RC (2010) Search and clustering orders of magnitude faster than BLAST, Bioinformatics 26(19), 2460-2461. doi: 10.1093/bioinformatics/btq461

UCHIME algorithm:Edgar,RC, Haas,BJ, Clemente,JC, Quince,C, Knight,R (2011) UCHIME improves sensitivity and speed of chimera detection, Bioinformatics doi: 10.1093/bioinformatics/btr381 [PMID 21700674].

UPARSE algorithm:Edgar, R.C. (2013) UPARSE: Highly accurate OTU sequences from microbial amplicon reads, Nature Methods [Pubmed:23955772, dx.doi.org/10.1038/nmeth.2604].


4、OTU代表序列分类学注释

RDP Classifier v2.11(https://sourceforge.net/projects/rdp-classifier/)Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.Appl Environ Microb 73(16): 5261-5267.


5、多样性指数

mothur(v.1.35.0) 'summary.single' command

Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.


6、稀释性曲线和Shannon-Wiener曲线

mothur(v.1.35.0) 'rarefaction.single' command

Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.


7、Rank-Abundance曲线

R语言(v2.12.1)进行数据运算和制作

Scott T Bates, Jose C Clemente, et al. Global biogeography of highly diverse protistan communities in soil. The ISME Journal (2013) 7, 652–659; doi:10.1038/ismej.2012.147.


8、  Specaccum物种累积曲线

R语言(v2.12.1)进行数据运算和制作

Maughan H, Wang PW, Diaz Caballero J, Fung P, Gong Y, et al. (2012) Analysis of the Cystic Fibrosis Lung Microbiota via Serial Illumina Sequencing of Bacterial 16S rRNA Hypervariable Regions. PLoS ONE 7(10): e45791. doi:10.1371/journal.pone.0045791.


9、OTU分布Venn图

R语言(v2.12.1)进行数据运算和制作

Fouts DE, Szpakowski S, Purushe J, Torralba M, Waterman RC, et al. (2012) Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen. PLoS ONE 7(11): e48289. doi:10.1371/journal.pone.0048289.


10、PCA分析

R语言(v2.12.1)中的PCA统计和分析函数

Yu Wang, Hua-Fang Sheng, et al. Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags. Appl. Environ. Microbiol. 2012, 78(23):8264. DOI: 10.1128/AEM.01821-12.


11、PCoA分析

R语言(v2.12.1)中的PCoA统计和分析函数

Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S Language. Wadsworth & Brooks/Cole.


12、NMDS分析

R语言(v2.12.1)vegan包(v2.0-1)中的NMDS分析与作图

Magali Noval Rivas, PhD, Oliver T. Burton, et al. A microbita signature associated with experimental food allergy promotes allergic senitization and anaphylaxis. The Journal of Allergy and Clinical Immunology.Volume 131, Issue 1 , Pages 201-212, January 2013.


13、群落结构Bar图和Pie图

R语言(v2.12.1)进行数据运算和制作

Lisa Oberauner, Christin Zachow, Stefan Lackner, et al. The ignored diversity: complex bacterial communities in intensive care units revealed by 16S pyrosequencing. SCIENTIFIC REPORTS. 3 :1413 .DOI: 10.1038/srep01413.(2013).


14、样本聚类树与柱状图组合分析

R语言(v2.12.1)进行数据运算和制作


15、群落Heatmap图

R语言(v2.12.1)vegan包(v2.0-1),vegdist和hclust进行距离计算和聚类分析

Elie Jami, Adi Israel, et al. Exploring the bovine rumen bacterial community from birth to adulthood. The ISME Journal advance online publication, 21 February 2013; doi:10.1038/ismej.2013.2.


16、 OTU Table抽平

mothur(v.1.35.0) 'sub.sample' command

Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.


17、Plsda分析

R语言(v3.2.3)mixOmics包(v5.2.0)中的plsda分析和作图

Perez-Enciso, M. and Tenenhaus, M. (2003). Prediction of clinical outcome with microarray data: a partial least squares discriminant analysis (PLS-DA) approach. Human Genetics 112, 581-592.


18、DCA、RDA、CCA分析

R语言(v2.12.1)vegan包(v2.0-1)中的DCA、RDA、CCA分析。

Sheik CS, Mitchell TW, Rizvi FZ, Rehman Y, Faisal M, et al. (2012) Exposure of Soil Microbial Communities to Chromium and Arsenic Alters Their Diversity and Structure. PLoS ONE 7(6): e40059. doi:10.1371/journal.pone.0040059.


19、Krona结果展示

KronaTools-2.6.1中的ktImportText命令

Interactive metagenomic visualization in a Web browser, Brian D Ondov, Nicholas H Bergman and Adam M Phillippy, BMC Bioinformatics201112:385, DOI: 10.1186/1471-2105-12-385


20、ANOSIM相似性分析

R语言(v2.12.1)vegan包(v2.0-1)中的ANOSIM分析

Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. Australian Journal of Ecology 18, 117-143.


21、Adonis多因素方差分析

R语言(v2.12.1)vegan包(v2.0-1)中的Adonis分析

Anderson, M.J. 2001. A new method for non-parametric multivariate analysis of variance. Austral Ecology, 26: 32–46.


22、Metastat物种丰度差异分析

mothur(v.1.35.0) 'metastats' command

Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.


23、LEfSE分析

LEfSE(v1.0)软件(https://bitbucket.org/biobakery/biobakery/wiki/lefse)

Segata N, Izard J, Waldron L, Gevers D, Miropolsky L et al. (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12: R60.10.1186/gb-2011-12-6-r60 PubMed: 21702898.


24、系统发生进化树构建

Muscle(v3.8.31)和FastTree(v2.1.8)

Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 32(5):1792-1797 .

Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics, (5) 113.

Price MN, Dehal PS, Arkin AP (2010) FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE 5(3): e9490. doi:10.1371.journal.pone.0009490.


25、(un)WeightedUniFrac分析

Qiime(v1.9.0)中的 'beta_diversity.py' 脚本

Tanya Yatsunenko, Federico, et al. Human gut microbiome viewed across age and geography. Nature 486, 222–227 (14 June 2012) doi:10.1038.nature11053.

Micah Hamady, Catherine Lozupone and Rob Knight. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. The ISME Journal (2010) 4, 17–27; doi:10.1038/ismej.2009.97.


26、样本距离箱式图

Qiime(v1.9.0)中的 'make_distance_boxplots.py' 脚本

Abrahamsson T.R., Jakobsson H.E., Andersson A.F., Bjorksten B., Engstrand L., Jenmalm M.C. Low diversity of the gut microbiota in infants with atopic eczema. (2012) Journal of Allergy and Clinical Immunology, 129(2).