Hello, Daniel!
Do you have some idea when you will release the new mapping database? I’m asking it because when I ran my shotgun samples against a new version of NCBI-nr (november 2021) using DIAMOND and after meganized them, I realized that all eukaryota assignments in taxonomic tree were generic while the Bacteria assignments were more specific. For example, I had 32,969 assignments to Opisthokonta (in the tree) and no subclades; however, when you check this clade in the “Inspect” tool, there are several specific assignments for different species (e.g Alternaria alternata and others). Researching in the forum, I guess that a new database could solve this specific question. There is another topic in the forum that is related to this - MEGAN sorting all alignments as unclassified -
Regards,
Fabyano Lopes