POCP-VS-AAI

Evaluation of POCP VS AAI: This is a R script to parse all the results from EzAAI and Bio-PI POCP matrix into summary tables, analyze them and create some plots.

Dependencies

The script has been evaluated in R v.4.2.2. It has the following R dependencies:

• dplyr
• tidyr
• vioplot
• ggplot2
• stringr
• car
• xlsx

How to run it

Download the repository. Open the script "AAI VS POCP.R" with R or Rstudio and change the "path_POCP_AAI" in the second line to the folder with the contents of the repository (it should contain a folder called pocp and aai with all the output files from the comparisons). Once the "path_POCP_AAI" is changed run the script. It should create a folder in the path_POCP_AAI path called results, with the summary files in XLSX and the plots in PDF.

Additional files in the repository not necessary for the script to run

• Accession table.txt: contains all the NCBI accession numbers of the genomes used in the analysis
• results: this folder contains all the outputs from the script.