Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jan 1;39(1):btac776.
doi: 10.1093/bioinformatics/btac776.

Pharokka: a fast scalable bacteriophage annotation tool

George Bouras  1   2 , Roshan Nepal  1   2 , Ghais Houtak  1   2 , Alkis James Psaltis  1   2 , Peter-John Wormald  1   2 , Sarah Vreugde  1   2
Affiliations

Pharokka: a fast scalable bacteriophage annotation tool

George Bouras et al. Bioinformatics. .

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.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Pharokka workflow. (A) An input phage complete assembly or input phage contigs are loaded. (B) CDS are predicted with PHANOTATE (default) or Prodigal. (C) CDS are functionally annotated by matching them to the PHROGs database with mmseqs2. The CDS are then matched to the CARD and the VFDB. (D) tRNAs, tmRNAs and CRISPRs are detected using tRNAscan-SE, Aragorn and MinCED. (E) All annotations are amalgamated into standards compliant output formats
See this image and copyright information in PMC

References

    1. Alcock B.P. et al. (2020) CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res., 48, D517–D525. - PMC - PubMed
    1. Al-Shayeb B. et al. (2020) Clades of huge phages from across earth’s ecosystems. Nature, 578, 425–431. - PMC - PubMed
    1. Arndt D. et al. (2016) PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res., 44, W16–W21. - PMC - PubMed
    1. Aziz R.K. et al. (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics, 9, 75. - PMC - PubMed
    1. Beamud B. et al. (2022) Genetic determinants of host tropism in Klebsiella phages. 10.1101/2022.06.01.494021. - DOI - PMC - PubMed

Publication types