Prototype code for identifying novel effectors from fusarium oxysporum unique genes. It starts from the raw fasta files 'core_Fo_genes_with_SP.fasta' and 'lycopersici_unique_with_SP.fasta' contained in a directory named 'raw_fasta'. The code is a mixture of bash scripts and Quarto notebooks (with R script alternatives available for the Quarto notebooks). These should be run in order and contain documentation within.
It is reccomended this workflow is ran on a cluster with a GPU to speed up the computational and creation of structure models using colabfold.
The analysis requires two key pieces of software to be installed (in addition to a standard Rstudio set-up):