Prokka pipeline

Prokka specifications


Unique identifier OMICS_04220
Name Prokka
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



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  • person_outline Torsten Seemann <>

Publication for Prokka

Prokka IN pipelines

PMCID: 5834339
PMID: 29496843
DOI: 10.1128/genomeA.01487-17

[…] carlsbad, ca, usa) at 38.4 ng/µl. the 576,285 high-quality paired-end reads were trimmed and then assembled using the spades assembler program (3). the draft genome sequence was annotated using prokka software (4). functional annotation was achieved using the blastp algorithm (5) against the clusters of orthologous groups (cogs) database and the rapid annotations using subsystems technology […]

PMCID: 5920174
PMID: 29700155
DOI: 10.1128/genomeA.00324-18

[…] swb005) in length, and the g+c contents are 68.1% and 69.5% (difference, 1.4%), respectively. automatic annotation and identification of rrna and trna genes were performed using the software tool prokka (9). this yielded 2 rrna genes, 78 trna genes, 3,682 protein-encoding genes with function prediction, and 3,265 genes coding for hypothetical proteins for strain swb005 and 4 rrna genes, 57 […]

PMCID: 5216340
PMID: 28057934
DOI: 10.1038/srep40206

[…] the raw data for each bacterium were error-corrected and assembled using spades 3.6.226. the final assemblies were filtered to contain ≥200 bp contigs. genome annotation was performed using prokka 1.1127. pan genome analysis was performed by get_homologues software28, using the standard described by tettelin and collaborators29., the whole genome sequences of 17 strains achieved […]

PMCID: 5381665
PMID: 28391322
DOI: 10.1093/gbe/evx001

[…] to the mtbc or m. leprae, which are not known to harbor plasmids, were downloaded and assembled using plasmidspades v 3.5.0 (antipov et al. 2016). resulting plasmid contigs were annotated using prokka v 1.11 (seemann 2014). plasmids with at least one annotated esx gene were chosen for further quality control processing, including checking for at least three esx genes, checking that all esx […]

PMCID: 5386241
PMID: 28394899
DOI: 10.1371/journal.pone.0175330

[…] whether various gene prediction algorithms caused artificial genetic diversity or whether indels/mutations caused frameshift, premature stop codon, or stop codon readthrough. we used the stand-alone prokka program [17] to re-annotate 20 complete genome sequences (table 1), excluding nitr202 strain due to unexpected nucleotide designations. based on roary results [18], the core genome included […]

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.