funannotate¶

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.

This module also includes iprscan/5.72 (interproscan.sh), repeatmasker/4.1.7.p1, repeatmodeler/2.0.3, iqtree/2.1.2, signalp6/6.0h, and CodingQuarry/2.0 dependencies.

If CodingQuarry prediction using stringtie alignments is desired, use the following in your job script:

export QUARRY_PATH="/apps/funannotate/1.8.17.1/opt/codingquarry-2.0/QuarryFiles"

Environment Modules¶

Run module spider funannotate to find out what environment modules are available for this application.

Environment Variables¶

HPC_FUNANNOTATE_DIR - installation directory
HPC_FUNANNOTATE_BIN - executable directory
FUNANNOTATE_DB - funannotate database directory
GENEMARK_PATH - genmark directory

Additional Usage 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

Categories¶

genomics, annotation, phylogenetics