Phage Genome Annotation

Once a complete phage genome/contig has been found, this can then be annotated. As a first pass annotation, we will use PROKKA and a custom database with vB_Eco_PIG.fa as the example phage. With a pre-registered locustag of PIGZ .

prokka --cpus 16 --usegenus --genus Caudovirales --prefix vB_Eco_PIG   --locustag PIGZ vB_Eco_PIG.fa

The folder vB_Eco_PIG will contain the output files
-Yes I know “Caudovirales” is not a genus. It is just a custom database and this is how it fits into Prokka
To create your own database of Caudovirales the files are here

Put them in the genus folder of Prokka installation
To also annotate with pVOGs the following can be used

 perl ~/Documents/scripts/ vB_Eco_PIG.gbk vB_Eco_PIG.embl 

This first converts to an embl file format from genbank
Then add VOG annotations

 perl ~/Documents/scripts/ vB_Eco_PIG.faa vB_Eco_PIG.embl 

This will update the embl file with VOG annotations.It will also produce a file called hmmVOG.txt that contains tab format of top VOG hits. This information is used to add annotation.
This is NOT the final annotation