LCA Parameters for viral metagenomics


I recently sequenced viruses in stool and serum from marine mammals using the minION. I am comparing two different de novo assemblers, CANU and Flye and running medaka polishing on all the assembled contigs. I ran blastx (e value <10^04) on all my assembled contigs and I am analyzing my aligned reads using MEGAN-LR. I was wondering what LCA parameters folks are using to detect known and unknown (novel) viruses using shot-gun metagenomic sequencing?