Pharokka: a fast scalable bacteriophage annotation tool

In recent years, there has been an increasing interest in bacteriophages, which has led to growing num-bers of bacteriophage genomic sequences becoming available. Consequently, there is a need for a rapid and con-sistent 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 min to run for an average 50-kb bacteriophage genome.