Prokka protocols

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Prokka specifications

Information


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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Publication for Prokka

Prokka in pipelines

 (233)
2018
PMCID: 5908941
PMID: 29674534
DOI: 10.1128/genomeA.00212-18

[…] the strain s-137 draft genome was assembled into 25 scaffolds composed of 142 contigs, with a total size of 9,465,473 bp and a gc content of 67.1%. automatic annotation was performed with prokka version 1.12 (). the genome presents two repeat regions and is predicted to encode 8,658 genes, including 8,582 protein-coding genes and 76 rna genes, including 66 trnas, 1 transfer-messenger […]

2018
PMCID: 5909648
PMID: 29579234
DOI: 10.1093/femsle/fny069

[…] was polished with racon (vaser et al.) and pilon (walker et al.). the quality of both assemblies was assessed with quast (gurevich et al.)., the ion pgm and the hybrid assemblies were annotated with prokka (seemann ) using a custom protein database built from the pseudomonas genus. the annotations were then searched for prophages using phaster (arndt et al.), and genomic islands using […]

2018
PMCID: 5822708
PMID: 29420776
DOI: 10.1093/gbe/evy033

[…] either to bacteria or previously identified plasmids and generally had average per base read coverage that was higher than observed in chromosomal scaffolds., coding regions were identified using prokka (), which uses prodigal () for cds prediction, rnammer () for ribosomal genes, aragorn () for trnas, signalp () for signal peptides, and infernal () for noncoding rnas. functional annotation […]

2018
PMCID: 5822837
PMID: 29479501
DOI: 10.7717/peerj.4402

[…] resistance database () was used as target and the 35-genome dataset as query. in addition, each genome was re-annotated using the same methodology to identify syntenic genes based on bacmet and prokka annotation without the bias of different annotation labels as implemented in prokka v1.12 (). finally, the results were visualized in their genomic context using the in-house script […]

2018
PMCID: 5824064
PMID: 29263205
DOI: 10.1128/JCM.01520-17

[…] an ast-p607 card. dna was extracted using a qiaxtractor (qiagen), and sequencing was performed on an illumina hiseq 2000 instrument. sequence reads were assembled using velvet and annotated using prokka. the pangenome was estimated using roary () with a 98% identification (id) cutoff. the van gene in the two patients with genetically related vrefm and vsefm isolates was extracted […]


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Prokka in publications

 (862)
PMCID: 5964442
DOI: 10.1128/mSystems.00025-18

[…] 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 (, ). […]

PMCID: 5946036
PMID: 29748402
DOI: 10.1128/genomeA.00352-18

[…] contigs (>500 bp) and a single scaffold. all gaps were closed by sequencing of gap-spanning pcr products using an abi 3730 dna analyzer (applied biosystems). genome annotation was performed using prokka ()., the genome of strain ym18 consists of a 3,726,411-bp chromosome with a g+c content of 60.7%. no plasmids were found. the chromosome contains 2 rrna operons, 49 trna genes, and 3,327 […]

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

[…] 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 […]

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

[…] 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 […]

PMCID: 5946039
PMID: 29748407
DOI: 10.1128/genomeA.00396-18

[…] of 3,332,539 bp. the average genome coverage of the paired-end reads was 121×. the maximum contig length was 701,368 bp. the draft genome of “ca. p. bacilliformis” botryco-2 was annotated using prokka version 1.12 (). the genome comprised 3,125 predicted protein-coding sequences (cdss), including 1,250 hypothetical proteins and 45 rnas. the g+c content of the genome was 56.91%. bacterial […]


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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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Desktop
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.