Please use this identifier to cite or link to this item:
https://hdl.handle.net/2440/137227
Citations | ||
Scopus | Web of Science® | Altmetric |
---|---|---|
?
|
?
|
Type: | Journal article |
Title: | Pharokka: a fast scalable bacteriophage annotation tool |
Author: | Bouras, G. Nepal, R. Houtak, G. Psaltis, A.J. Wormald, P.-J. Vreugde, S. |
Citation: | Bioinformatics, 2023; 39(1):1-4 |
Publisher: | Oxford University Press (OUP) |
Issue Date: | 2023 |
ISSN: | 1367-4803 1367-4811 |
Editor: | Marschall, T. |
Statement of Responsibility: | George Bouras, Roshan Nepal, Ghais Houtak, Alkis James Psaltis, Peter-John Wormald, and Sarah Vreugde |
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/phar okka). Pharokka has been tested on Linux-64 and MacOSX machines and on Windows using a Linux Virtual Machine. |
Keywords: | Bacteriophages Computational Biology Genomics Genome Software |
Rights: | © The Author(s) 2022. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
DOI: | 10.1093/bioinformatics/btac776 |
Grant ID: | http://purl.org/au-research/grants/nhmrc/1196832 |
Published version: | http://dx.doi.org/10.1093/bioinformatics/btac776 |
Appears in Collections: | Medicine publications |
Files in This Item:
File | Description | Size | Format | |
---|---|---|---|---|
hdl_137227.pdf | 406.92 kB | Adobe PDF | View/Open |
Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.