Spliced genes + ncRNAs

[joanmarticarreras]

Hi Ryan,

Great tool! I've been using it for a couple of side projects and seems to work great (python3 version). However, now I want to submit some human cytomegalovirus genomes (HCMV) and I found myself in a bit of a mess (correcting everything manually).

Apparently VAPiD has troubles with transferring ncRNA and repeats, which makes the gene name/count (ie UL2, UL3, UL4, etc) to shift some positions. Additionally, I've found that performs rather poorly with genes with multiple CDS that require splicing.

Both cases a quite relevant for dsDNA viruses and I hope you'll consider an update of VAPiD in order to fulfill better those cases. If you need some examples to work with, I recommend you use any of the HCMV available genomes.

EDIT: I recommend to run it back to back with RATT (which now can be installed through Conda without much hassle) + gbd2tbl + tbl2asn

[rcs333]

Hi Joan,

Great to hear from you! I hope all is well with you!

VAPiD performs really really poorly with all of the herpes viruses, this is partially because a different member of our group handled all of the HHV genomes and also because as I'm sure you're aware they do some pretty crazy stuff with the ncRNAs, repeats, and splicing. All RNA splicing is hard coded, so I would need to make a pretty significant update to get it working with VAPiD.

Unfortunately for VAPiD I'm currently in medical school and don't have a lot of time for software development at this time :(

This is the link for the HHV-6 assembly pipeline that I'm pretty sure is still used.
https://github.com/proychou/HHV6

She also has several other herpes virus annotation pipelines.
https://github.com/proychou?tab=repositories

These might help or they might not, I'm sorry I can't do more for you. I recently annotated a giant crAssphage with VAPiD and it basically didn't put any of the genes in the right place but it did create the necessary inputs for tbl2asn which made manually fixing the tbl for annotation and submission a lot easier than it would have been.

I will keep this issue open so if I do get some time to work on development I can work on this but I won't have time to work on VAPiD in the near future.

Hopefully some of this is helpful, good luck and happy annotating!!!