Difference between revisions of "Prokka"
Jump to navigation
Jump to search
(Created page with "Category:Software {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|prokka}} |{{#vardefine:url|http://www.vicbioinformatics.com/software.prokka.shtml}} <!--CONFIGURATION:...") |
|||
| (4 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]] | + | [[Category:Software]][[Category:Biology]][[Category:Assembly]][[Category:Genomics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|prokka}} | |{{#vardefine:app|prokka}} | ||
| Line 25: | Line 25: | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | < | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 19:41, 21 August 2022
Description
Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA.
Environment Modules
Run module spider prokka to find out what environment modules are available for this application.
System Variables
- HPC_PROKKA_DIR - installation directory
Citation
If you publish research that uses prokka you have to cite it as follows:
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014 Jul 15;30(14):2068-9. PMID:24642063