Prokka Files

Rapid prokaryotic genome annotation

This is an exact mirror of the Prokka project, hosted at https://github.com/tseemann/prokka. SourceForge is not affiliated with Prokka.

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Name	Modified	Size	InfoDownloads / Week
Parent folder
Heading into the sunset source code.tar.gz	2025-12-14	70.9 MB	0
Heading into the sunset source code.zip	2025-12-14	71.1 MB	0
README.md	2025-12-14	1.7 kB	0
Totals: 3 Items		142.1 MB	0

The future

This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwengers instead - it's a great successor to Prokka without all the technical debt from what was my first real bioinformatics tool. Keep on annotatiing! :-)

Major changes

Removed all bundles binaries - please use bioconda or environment.yml
New sprot DBs for bacteria, archaea, viruses
New HAMAP HMMs for bacteria, archaea
Support gzip compressed HMMs
New internal database update system I can use
Removed support for Homebrew
Moved TRAIVIS-CI to Github Actions

Pull requests accepted

Link --proteins section of manual to fasta-db-format section by @0xaf1f in https://github.com/tseemann/prokka/pull/611
Prodigal: don't set metagenome mode if training file given by @jvolkening in https://github.com/tseemann/prokka/pull/538
Use version objects for version cmp by @kiwiroy in https://github.com/tseemann/prokka/pull/517
Speed up overlap lookup in CDS stage by @fluhus in https://github.com/tseemann/prokka/pull/493

New Contributors

@0xaf1f made their first contribution in https://github.com/tseemann/prokka/pull/611
@jvolkening made their first contribution in https://github.com/tseemann/prokka/pull/538
@kiwiroy made their first contribution in https://github.com/tseemann/prokka/pull/517
@fluhus made their first contribution in https://github.com/tseemann/prokka/pull/493

Full Changelog: https://github.com/tseemann/prokka/compare/v1.4.14.5..v1.15.6

Source: README.md, updated 2025-12-14

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