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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
BioPerl, BLAST, HMMER, Aragorn, Prodigal, tbl2asn, GNU Parallel, Infernal
Maintained Yes




No version available

Publication for Prokka

Prokka citations


Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

PMCID: 5964442
DOI: 10.1128/mSystems.00025-18
call_split See protocol

[…] ttle amino acid identity between viral families. The taxon abundance data were extracted from MEGAN6 and imported into RStudio for visualization (). Genes on the assembled contigs were predicted with Prokka () using the settings --kingdom Viruses and an e value of 1e−5. Multiple alignments of genes and genomes were made in MEGA7 using the MUSCLE algorithm with default settings (, ). The alignments […]


Draft Genome Sequence of Staphylococcus aureus Strain HD1410, Isolated from a Persistent Nasal Carrier

Genome Announc
PMCID: 5946038
PMID: 29748411
DOI: 10.1128/genomeA.00411-18

[…] (). Contigs obtained from the assembly were therefore curated for length (>500 bp) and coverage (>10×) to ensure no errors and contamination in the draft genome. The contigs were then annotated using Prokka 1.12 (based on Genetic Code Table 11) () and the NCBI Prokaryotic Genome Annotation Pipeline.The multilocus sequence typing (MLST), VirulenceFinder, ResFinder, and PlasmidFinder (http://genomic […]


Draft Genome Sequence of a “Candidatus Brocadia” Bacterium Enriched from Activated Sludge Collected in a Tropical Climate

Genome Announc
PMCID: 5946052
PMID: 29748410
DOI: 10.1128/genomeA.00406-18

[…] igh completeness (98.8%) and low contamination rate (1.7%), and it was annotated to the marker set lineage UID2565, which is selective for “Candidatus Brocadiaceae.” We annotated predicted genes with Prokka (v1.10) (), finding that this draft genome sequence encodes 2,765 genes, 47 tRNAs, and 3 rRNA genes. Using the CheckM SSUfinder module (), one 16S gene of length 1,572 bp was identified from th […]


Profiling microbial strains in urban environments using metagenomic sequencing data

Biol Direct
PMCID: 5944035
PMID: 29743119
DOI: 10.1186/s13062-018-0211-z

[…] v1, ASM28295v1, PseStu2.0, ASM32706v1, PstNF13_1.0, PstB1SMN1_1.0, ASM59047v1, ASM66191v1, ASM95268v1, ASM98286v1, ASM103864v1, ASM106422v1, ASM127647v1, ASM157508v1) which were first annotated using Prokka [] and then clustered into gene-families with Roary []. We profiled the 1572 New York samples from the MetaSUB dataset with PanPhlAn version […]


The orphan germinant receptor protein GerXAO (but not GerX3b) is essential for L alanine induced germination in Clostridium botulinum Group II

Sci Rep
PMCID: 5935672
PMID: 29728678
DOI: 10.1038/s41598-018-25411-x
call_split See protocol

[…] For identification of gerX genes in the genomes of C. botulinum Group II strains, genome sequences were re-annotated using Prokka version 1.12. Roary version 3.5.7 was used for comparative genomics. Alignments were made with Clustal omega and MEGA version 6.0 and used for generation of phylogenetic trees using the Neighbo […]


Invasive Methicillin Resistant Staphylococcus aureus USA500 Strains from the U.S. Emerging Infections Program Constitute Three Geographically Distinct Lineages

PMCID: 5932375
PMID: 29720528
DOI: 10.1128/mSphere.00571-17
call_split See protocol

[…] Strains were assembled de novo using SPAdes v3.7.1 () and annotated using PROKKA v1.11 (). FASTQ sequencing output files from strains with more than 100× coverage were down-sampled using a custom script ( base […]


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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.