Prokka specifications


Unique identifier OMICS_04220
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements BioPerl, BLAST, HMMER, Aragorn, Prodigal, tbl2asn, GNU Parallel, Infernal
Maintained Yes


  • Eubacteria



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  • person_outline Torsten Seemann <>

Prokka article

Prokka citations

PMCID: 5764930

[…] in 43 to 197 contigs of >1 kb, and accounting for total genome sizes ranging from 4,578,015 to 5,285,335 bp (table 1). coding sequences (cdss) and orthologous genes were determined using prokka (v1.12) (7) and proteinortho (v5.15) (8). between 4,204 and 5,035 coding dna sequences were identified in the corresponding genomes (table 1). to predict and identify plasmids, serotypes, […]

PMCID: 5708674

[…] or “putative uncharacterized protein”. albeit many of the functions and products of these genes have been described since, for ease of discussion we re-annotated the genome using a combination of prokka [93], and searches in stringdb and blast (blastp and blastx). putative functions and expression profiles are summarised in s5 table. an overall summary of the m1 genome, including rods, […]

PMCID: 5637514

[…] for strain 080116a had a genome size of 5.63 mb (45.7% gc), 107 contigs (n50 = 275,484 bp), and a maximum contig size of 1,249,611 bp., gene predictions for the draft assemblies were performed using prokka version 1.11 (8) and rapid annotation using subsystem technology (rast) (9). there were 5,145, 5,542, and 5,205 coding sequences detected for strains re87, aic-7, and 080116a, respectively. […]

PMCID: 5626246

[…] european nucleotide archive (ena) repository under accession number erp018940 ( reads from the isolates were assembled using spades,57 annotated using prokka,58 and the core and pan-genome of the isolates was estimated using roary.59 the alignment of the core genome from roary was used as input to create a phylogenetic tree using raxml60 with 100 […]

PMCID: 5328535

[…] with the default settings. chromosomal contigs were removed by mapping against either dh10b, mg1655, or w3110 genome sequences using blast (14). the remaining plasmid contigs were annotated using prokka (15). screening for antimicrobial resistance genes was performed using resfinder (16). core and pan genome determination and whole-plasmid-based phylogeny were performed with roary (17), using […]

Prokka institution(s)
Victorian Bioinformatics Consortium, Monash University, Clayton; Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton, Australia
Prokka funding source(s)
This research was supported in part by the Victorian Life Sciences Computation Initiative, an initiative of the Victorian Government hosted by the University of Melbourne, Australia.

Prokka review

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Fast, accurate and easy to use. You could not ask more from an annotation pipeline. For visualization you can use other tools, but prokka is for sure the best annotation tool to start with.

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