Study title: Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub) species

Authors: J.E. Edwards*, S.A. Shetty, P. van den Berg, F. Burden, D.A. van Doorn, W.F. Pellikaan, J. Dijkstra and H. Smidt

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

This repository contains codes for analysis done in the research article by Edwards, J.E., Shetty, S.A., van den Berg, P., Burden, F., van Doorn, D.A., Pellikaan, W.F., Dijkstra, J. and Smidt, H. (2020). Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub) species. Animal Microbiome, 2(1), pp.1-16. link to article.

Structure:
EdwardsJ_2019_EquineCoreMicrobiome
project folder:

Structure:  
EdwardsJ_2019_EquineCoreMicrobiome/ # Main repository  
                     |---- Sequencing Barcode Tables_GitHub_21Feb2019.xlsx # Per sample barcode informaation.  
                     |---- bacterial_data_4Feb2019/ # Data and codes for bacterial and archeal community analysis.  
                              |--- codes/ 
                                     |---plot_taxa_boxplot_edit.R # code for plotting   
                              |--- ng_tax_output/ # otuput from NG-Tax  
                                     |--- all_otus.tree  
                                     |--- EAF002_16S_rerun.biom  
                                     |--- EAF002_16S_rerun_map.csv  
                              |--- phyloseq_rds/  
                                     |---  
                                     |---   
                              |--- bacterial data.RMD  
                     |---- fungal_data_4Feb2019/ # Data and codes for fungal community analysis.  
                              |--- codes/ 
                                     |---plot_taxa_boxplot_edit.R # code for plotting
                              |--- ng_tax_output/ # otuput from NG-Tax  
                                     |--- otu_merged_minus_18_NTC_nonAF_OTU.dnd    
                                     |--- EAF002_AF_150_06_Final_minus_OTU_rev_taxformat.biom    
                                     |--- EAF002_150_06minPerT_map.csv   
                              |--- phyloseq_rds/ 
                                     |---  
                                     |---  
                              |--- fungal_data.RMD