conda install and activate

conda install -c conda-forge -c bioconda -c defaults abricate

conda activate abricate

run abricate with virulent database

abricate --db vfdb <viral_contigs> > <abricate_output.tsv>

process output, sorting abricate contigs by number of virulent genes, coverage, identiy

python proc_abricate.py <abricate_output.tsv> <rank_contigs_virulence.tsv>