Prokka is a software tool that significantly simplifies the process of fully annotating a draft bacterial genome. With the advent of multiplex capability and the high yield of DNA sequencing instruments, bacterial whole genome sequencing has become a routine affair. However, annotating all relevant genomic features on the contigs can be time-consuming. Existing web- and email-based systems are not applicable for sensitive data or integrating into computational pipelines.

Prokka solves this problem by providing a command-line tool to fully annotate a draft bacterial genome in about 10 minutes using a typical desktop computer. The software produces standards-compliant output files that genome browsers can further analyze or view.


Genomics;Model organisms;Virology


  • Operation: Gene prediction;Coding region prediction;Genome annotation

  • Software interface: Command-line user interface

  • Language: Perl

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 1.14.5

  • Credit: The Victorian Life Sciences Computation Initiative, an initiative of the Victorian Government hosted by the University of Melbourne, Australia.

  • Input: FASTA

  • Output: .gff, .gbk, .fna, .faa, .ffn, .sqn, .fsa, .tbl, .err, .log, .txt, .tsv

  • Contact: Torsten Seemann

  • Collection: -

  • Maturity: Stable


Download and documentation

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