Pharokka: Fast Phage Annotation Tool
Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.
If you are looking for rapid standardised annotation of bacterial genomes, please use Bakta. Prokka, which inspired the creation and naming of pharokka, is another good option, but Bakta is Prokka’s worthy successor.
Quick Start
The easiest way to install pharokka is via conda:
conda install -c bioconda pharokka
Followed by database download and installation:
install_databases.py -o <path/to/databse_dir>
And finally annotation:
pharokka.py -i <phage fasta file> -o <output directory> -d <path/to/database_dir> -t <threads>
As of pharokka v1.4.0, if you want extremely rapid PHROG annotations, use --fast:
pharokka.py -i <phage fasta file> -o <output directory> -d <path/to/database_dir> -t <threads> --fast
Documentation
Check out the full documentation at https://pharokka.readthedocs.io.