Difference between revisions of "Funannotate"
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(Created page with "Category:Software {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|REPLACE}} |{{#vardefine:url|REPLACE}} <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> |{{#vardefin...") |
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| − | [[Category:Software]] | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
| − | |{{#vardefine:app| | + | |{{#vardefine:app|funannotate}} |
|{{#vardefine:url|REPLACE}} | |{{#vardefine:url|REPLACE}} | ||
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|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine: | + | |{{#vardefine:exe1|}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | If you are setting up funannotate for analysis you may have to run the following unannotate db setup job first: | |
| + | <pre> | ||
| + | |||
| + | if [[ ! -d config ]]; then | ||
| + | module purge; module load augustus | ||
| + | rsync -a $HPC_AUGUSTUS_CONF . | ||
| + | fi | ||
| + | |||
| + | export AUGUSTUS_CONFIG_PATH=$(pwd)/config | ||
| + | |||
| + | funannotate setup -i all --update -d ./funannotate_db | ||
| + | </pre> | ||
| + | |||
| + | Set the following environment variable in the job scripts for subsequent funannotate analyses. | ||
| + | export FUNANNOTATE_DB=$(pwd)/funannotate_db | ||
| + | |||
|}} | |}} | ||
Revision as of 15:52, 1 March 2022
Description
[REPLACE funannotate website]
Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. The impetus for this software package was to be able to accurately and easily annotate a genome for submission to NCBI GenBank. Existing tools (such as Maker) require significant manually editing to comply with GenBank submission rules, thus funannotate is aimed at simplifying the genome submission process.
Environment Modules
Run module spider funannotate to find out what environment modules are available for this application.
System Variables
- HPC_FUNANNOTATE_DIR - installation directory
- HPC_FUNANNOTATE_BIN - installation directory