Evaluation of funannotate

Analysed by: Lukas Jelonek

Research questions/topics

1. Gain knowledge about the annotation process with funannotate
2. Evaluate if the process can be automized

Research plan

1. Gather data for evaluation (contigs/scaffolds + rna-seq data)
2. Install funannotate
3. Annotate downloaded data with funannotate

Data and Software

P. cubensis

• Reasons: moderate size genome, rna-seq data available

• Assembly source: https://mycocosm.jgi.doe.gov/Psicub1_1/Psicub1_1.home.html

• RNA-Seq source (bgi-seq): https://www.ebi.ac.uk/ena/browser/view/PRJNA450675

funannotate

• Source: conda
• Documentation: https://funannotate.readthedocs.io/en/latest/

Analysis

The whole analysis is described by the nextflow workflow in main.nf. This workflow has a few dependencies that are not (yet) included and thus must be installed/configured beforehands.

Setup of funannotate

# install everything via conda
conda create --prefix <your-installation-target-directory> funannotate
conda activate --prefix <your-installation-target-directory>

# setup databases
export FUNANNOTATE_DB=/vol/funant/evaluate_funannotate/funannotate_dbs/

# install database by database as the interpro installation did not work
# and must be excluded
for i in merops uniprot dbCAN pfam repeats go mibig busco_outgroups gene2product
do 
  funannotate setup -w -i $i
done
funannotate setup -i busco -b dikarya

Setup of eggnogmapper

conda install eggnog-mapper
# funannotate had no option to configure the eggnog-mapper database-directory. I added 
# the possibility to configure the eggnog-mapper database-directory via an env-variable.
# It now has been merged to eggnog-mapper and should be available in future releases (
# see https://github.com/eggnogdb/eggnog-mapper/pull/220 )
export EGGNOG_DATA_DIR=/vol/funant/evaluate_funannotate/eggnog_db/
download_eggnog_data.py --data_dir $EGGNOG_DATA_DIR 

Run the workflow

nextflow run . -resume -with-report report.html -with-dag graph.html

Results

• results/ - the funannotate annoation output
• graph.html - the workflow graph
• report.html - the runtime report of the nextflow workflow