Pharokka: a fast scalable bacteriophage annotation tool

• Published in: Bioinformatics (Oxford, England) Vol. 39; no. 1
• Main Authors: Bouras, George, Nepal, Roshan, Houtak, Ghais, Psaltis, Alkis James, Wormald, Peter-John, Vreugde, Sarah
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2023; Oxford Publishing Limited (England)
• Subjects: Annotations; Applications Note; Availability; Bacteriophages - genetics; Computational Biology; Genome; Genomes; Genomics; Linux; Phages; Software; Source code; Virtual environments
• ISSN: 1367-4811; 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btac776

Abstract 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 min 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.