Contains code pipeline used for analysis in the paper "Tardigrade community microbiomes in North American orchards includes putative endosymbionts and plant pathogens" (Laura E. Tibbs-Cortes, Bienvenido W. Tibbs-Cortes, and Stephan Schmitz-Esser 2022, Frontiers in Microbiology). https://doi.org/10.3389/fmicb.2022.866930
Raw sequence data deposited at https://www.ncbi.nlm.nih.gov/bioproject/801902.
This folder contains the mothur output that will be read by the R code and a key (mothur_group_vs_sample_code.xlsx) to convert between the sample names used in Mothur and the Map file (in design subfolder).
To unzip the tar.gz file, type tar -xzvf mothur_output.tar.gz in a terminal.
This folder contains the experimental design data for each sample.
This folder contains code used. Use the tardigrade_microbiome_processing_clean.R script to process the mothur output (found in taxonomy folder). The config.toml file is used partway through the R file. The beta_diversity.R file was not used in the published analysis but was requested as follow-up to mooreryan/divnet-rs#3.
The file OTUs1to12761_formatted.fasta contains the consensus sequences for OTUs 1-12761. Posted March 9, 2023 upon request.