Pharokka: Fast Phage Annotation Tool

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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: -o <path/to/databse_dir>

And finally annotation: -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: -i <phage fasta file> -o <output directory> -d <path/to/database_dir> -t <threads> --fast


Check out the full documentation at