PHASTEST (PHAge Search Tool with Enhanced Sequence Translation) is a web server for the identification and annotation of prophage sequences in bacterial genomes. The program was created by the Wishart Research Group at University of Alberta (doi: 10.1093/nar/gkad382).
This repository contains scripts to help compare PHASTEST results for different genomes. An example dataset is included.
phastest-summary.R uses the summary.txt files generated by PHASTEST to tell you the percentage of each genome that is predicted to be phage derived. More summary information will be added in the future.
phastest-genetypes.R runs through a set of PHASTEST predictions and generates a stacked bar chart of the number of total predicted prophage genes and the number of each "type" of gene for each organism. It's important to note one major limitation of this workflow is that the gene "types" are relatively arbitrary. You're free to adjust them to better suit your own data.
For a more detailed walkthrough, see this code on Kaggle: https://www.kaggle.com/code/catherineryan/phastest-data-viz