Study title: Comparison of the faecal microbiota of different types of domesticated equines

Authors: J.E. Edwards*, A. Schennink, F. Burden, S. Long, D.A. van Doorn, W.F. Pellikaan, J. Dijkstra, E. Saccenti and H. Smidt

Correspondence: JE (joan.edwards[at]wur.nl)

This repository contains codes for analysis done in the research article by Edwards JE, et al (2019) Comparison of the faecal microbiota of different types of domesticated equines. Under review. XX.

Structure:
EdwardsJ_2019_Equine_Type_Comparison project folder:

Structure:  
EdwardsJ_2019_Equine_Type_Comparison/ # Main repository  
                     |---- Sequencing Barcode Tables.xlsx # Per sample barcode informaation.  
                     |---- EAF001_16S_GitHub/ # Data and codes for bacterial and archeal community analysis.  
                              |--- codes/ 
                                     |---plot_taxa_boxplot_edit.R # code for plotting boxplots   
                              |--- ng_tax_output/ # otuput from NG-Tax  
                                     |--- all_otus.tree  
                                     |--- Joan_Angeline_EAF001_16S.biom  
                                     |--- EAF001_16S_map.csv  
                              |--- Equine_Type_Comparison_16S.RMD  
                     |---- EAF001_AF_GitHub/ # Data and codes for anaerobic fungal community analysis.  
                              |--- codes/ 
                                     |---plot_taxa_boxplot_edit.R # code for plotting boxplots
                              |--- ng_tax_output/ # otuput from NG-Tax  
                                     |--- otu_m_minus_17109272.dnd    
                                     |--- EAF001_150_06minPerT_biom_FINAL_rev_tax.biom    
                                     |--- EAF001_150_06minPerT_map.csv   
                              |--- Equine_Type_Comparison_AF.Rmd