Examples

Complete annotation

python ensembl_anno.py \
    --genome_file genome.fa \
    --output_dir output \
    --run_full_annotation

Transcriptome only

python ensembl_anno.py \
    --run_transcriptomic \
    --short_read_fastq_dir reads/

Protein annotation

python ensembl_anno.py \
    --run_genblast \
    --protein_file proteins.fa