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AnantharamanLab / VIBRANT

Virus Identification By iteRative ANnoTation
GNU General Public License v3.0
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AMGs annotation suitable for diverse viral genomes? #47

Open ChenTianYi99 opened 3 years ago

ChenTianYi99 commented 3 years ago

Hi, thanks in advance. I have obtained multiple viral sequences identified by several tools, including vibrant. Now, i want to find AMGs. But it seems that vibrant could only annotate sequences identified by itself and other sequences were ignored. Besides, you said that this tool was mainly designed for bacterial and archaeal viruses. So does this mean that vibrant is not suitable for annotation of diverse viral genomes (RNA, NCLDV or other eukaryotic virus) ? Looking forward to your reply.

KrisKieft commented 3 years ago

Hi,

VIBRANT is built as a virus identification tool that will annotate the sequences it identifies, rather than an annotation tool. One option is to annotate your other viral sequences identified by other tools and then manually identify the AMGs. VIBRANT comes with a list of KEGG annotations designated as AMGs, which can be found in the files folder.

VIBRANT is not suitable for eukaryotic viruses and I have not specifically checked NCLDVs. It will identify some of them but the recall rate is very low. If the RNA virus is a bacterial/archaeal virus then VIBRANT may identify it, but again the recall is about 50% based on my tests (eukaryotic virus is lower).