This setup and R script is to create a customizeable visualization of genome information.
As a prerequisite, you have to annotate your genome sequence with kbase with Annotation Apps such as RAST or Prokka. When done, export the annotation as json file on the export menu of your genome annotation.
Next, run the first part of the Rscript circos_genome.R to create a protein fasta file with the amino acid sequences for each gene. You can then upload this fasta file on BlastKOALA to annotate the KEGG Orthology (KO) ID for each gene. The output of this process (will take a while to send to you by the web service) is a text file with the gene id and the KO id.
Now you basically have all of the things neccessary to plot your genome. Let me just quickly summarize again what you need:
- Genome sequence as fasta file
- Genome annotation as json file from kbase
- Gene to KO id translation table from BlastKOALA
If you have all these items, you can proceed with the other parts of the Rscript circos_genome.R.