Difference between revisions of "Prokka"

Revision as of 20:36, 10 June 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

@@ Line 25: / Line 25: @@
 <!--Modules-->
-==Required Modules==
+==Environment Modules==
-===Serial===
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* {{#var:app}}
-<!--
-===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
 * HPC_{{uc:{{#var:app}}}}_DIR - installation directory
@@ Line 80: / Line 70: @@
 <!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 __NOTOC____NOEDITSECTION__
-=Validation=
-* Validated 4/5/2018