Add new vOTUs databases from other sampling compartments

[mhmism]

Hello,

I have a shotgun dataset of combined fecal and oral samples. I would like to use phanta, however, it might be only suitable for the fecal samples. I would like to know how to include additional vOTUs to the phanta db to also include phages/viruses coming from other sampling compartments.

Here is an example of vOTUs databases, I am interested to incorporate:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9160773/
https://pubmed.ncbi.nlm.nih.gov/36399502/

Is there a simple straightforward way for this?

[meenachakra]

Hi! Thanks for your interest. For now we recommend using Phanta for human gut samples only.

To answer your question, it's doable but not totally straightforward. The hardest thing about creating the DB is updating the taxonomic relationships. You'll have to not only add the branches for the new viruses but also make sure that you don't add branches that are already there for the MGV/RefSeq viruses. We hope to add a tutorial over the next few weeks on how to customize the DB, however it is a bit tricky.

[CarsonJM]

Hi @meenachakra I was wondering if you have any update on adding this tutorial? Since the UHGV classify tool has been released (https://github.com/snayfach/UHGV) I am wondering if assigning taxonomy to novel sequences with this tool could aide in adding new viral sequences. I'd be happy to do some testing on my end if that would help!

[meenachakra]

Hi Carson, Unfortunately we never got around to doing this! We do hope to complete such a tutorial over the next few months. In the meantime, if you have questions about your specific scenario, please feel free to email us
mchakra@stanford.edu
yishay@stanford.edu