Hi,

I was wondering, what is the common use of the Kraken2 nucleotide database? Is it used to improve accuracy of classification and help map unmapped reads?

I am wondering as I want to search against a large database of organisms, many of which don't have assembled genomes, so I was hoping that adding any available nucleotide sequences for those organisms (in addition to the assembled genomes of the few that have them) would improve the classification power of Kraken2. I am using a custom database. Is this appropriate, and would it help my classification?