Question: Is it possible to include >1 unclassified genome in 1 single run of `similar_viruses`?

[patriciatran]

Hello,

Thanks for making this pipeline! I was able to run the pipeline similar_viruses following the instructions in your guide (I used the GUI option). For the GenomeDescTableFile parameter, I suppose we could add more rows corresponding to the extra genomes to create the vmr.csv file.

I wasn't able to find an option to include >1 genome as the GenomeSeqFile option in the documentation - is that a possibility?

I would be interested in having a figure like Pphmm_locations.pdf that summarize the info from multiple closely related genomes that I run through gravity2.

Thanks for the info!

[Mayne941]

Hi, many thanks for your feedback!

Yes, you should be able to include >1 unclassified genome in a single run of /similar_viruses/. When running /convert_fasta_to_genbank_and_vmr/ (step 3 in the guided example), you can have as many sequences in the input fasta file ("fasta_fname") as you need. These will be copied into the GenBank file ("GenomeSeqFile" for the similar viruses pipeline) and should be evaluated simultaneously. Let me know how you get on with this.

I'd be very happy to look at an additional feature on the next GRAViTy-V2 release. Could you please expand a little on what you'd like the pphmm_locations graph to show?

Feel free to email me if you want to send any attachments - my contact address can be found in the article.

Best - Rich