Pharokka: a fast scalable bacteriophage annotation tool.

SUMMARY
In recent years, there has been an increasing interest in bacteriophages which has led to growing numbers of bacteriophage genomic sequences becoming available. Consequently, there is a need for a rapid and consistent genomic annotation tool dedicated for bacteriophages. Existing tools either are not designed specifically for bacteriophages or are web- and email- based and require significant manual curation, which makes their integration into bioinformatic pipelines challenging. Pharokka was created to provide a tool that annotates bacteriophage genomes easily, rapidly and consistently with standards compliant outputs. Moreover, Pharokka requires only two lines of code to install and use and takes under 5 minutes to run for an average 50 kb bacteriophage genome.


AVAILABILITY AND IMPLEMENTATION
Pharokka is implemented in Python and is available as a bioconda package using 'conda install -c bioconda pharokka'. The source code is available on GitHub (https://github.com/gbouras13/pharokka). Pharokka has been tested on Linux-64 and MacOSX machines, and on Windows using a Linux Virtual Machine.


SUPPLEMENTARY INFORMATION
All benchmarking input FASTA and output files, including the python script calc_gff_coding_density_prokka.py script, is available at https://doi.org/10.5281/zenodo.7227091.