Abstract
Abstract Summary: The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. Availability and implementation: Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/ . Contact: torsten.seemann@monash.edu
Keywords
PerlComputer scienceGenomeContigAnnotationMIT LicenseSoftwareSequence assemblyGenome projectBacterial genome sizeComputational biologyOpen sourceWorld Wide WebBiologyGeneticsProgramming languageArtificial intelligenceGene
Affiliated Institutions
Related Publications
Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline
Abstract Background Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current...
Primer3Plus, an enhanced web interface to Primer3
Here we present Primer3Plus, a new web interface to the popular Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. Primer3 con...
Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology
Translating the Oxford Nanopore MinION sequencing technology into medical microbiology requires on-going analysis that keeps pace with technological improvements to the instrume...
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today's sequencing and array-based profiling ...
Ensembl 2015
Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model orga...
Publication Info
- Year
- 2014
- Type
- article
- Volume
- 30
- Issue
- 14
- Pages
- 2068-2069
- Citations
- 17639
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
17639
OpenAlex
Cite This
Torsten Seemann
(2014).
Prokka: rapid prokaryotic genome annotation.
Bioinformatics
, 30
(14)
, 2068-2069.
https://doi.org/10.1093/bioinformatics/btu153
Identifiers
- DOI
- 10.1093/bioinformatics/btu153