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
http://s3.climb.ac.uk/ADM_share/Caudovirales.psq
http://s3.climb.ac.uk/ADM_share/Caudovirales.psq
http://s3.climb.ac.uk/ADM_share/Caudovirales.tar.gz

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

 perl ~/Documents/scripts/genbank_2_embl.pl 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/update_embl_with_hmm_VOG.pl 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