Difference between revisions of "Funannotate"

Latest revision as of 16:51, 15 August 2022

Description

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

Additional Information

If you are setting up funannotate for analysis you may have to run the following unannotate db setup job first:


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

Set the following environment variable in the job scripts for subsequent funannotate analyses.

export FUNANNOTATE_DB=$(pwd)/funannotate_db

@@ Line 1: / Line 1: @@
-[[Category:Software]]
+[[Category:Software]][[Category:Phylogenetics]]
 {|<!--CONFIGURATION: REQUIRED-->
-|{{#vardefine:app|REPLACE}}
+|{{#vardefine:app|funannotate}}
-|{{#vardefine:url|REPLACE}}
+|{{#vardefine:url|https://github.com/nextgenusfs/funannotate}}
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 |{{#vardefine:job|}}            <!--JOB SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
@@ Line 34: / Line 34: @@
 {{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+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
 |}}