I’m using pharokka to annotate phage genomes and would like to visualize them for a figure. How would I do this given the output files from the program?
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Welcome, @danielellisco
You could use JBrowse, and we have some tutorials that can help.
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Example using outputs from different tools, but the overall process is the same. Customize any data manipulations to fit the data you have – these are mostly about cleaning up file formats and simplifying items like contig identifiers. → Hands-on: Bacterial Genome Annotation / Bacterial Genome Annotation / Genome Annotation
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If you are new to manipulating file formats, this is a good “cheat sheet” for common tools. Hands-on: Data Manipulation Olympics / Data Manipulation Olympics / Introduction to Galaxy Analyses
And, you could explore using Circos, too!
Hope this helps! 