I've read the manual, but I'm still confused. Does Kraken2 break up the reads you give it into 31-32 KMERS and looks for matches against its database? If that's the case, does this mean it gives a couple nucleotide mismatches? Also, how does this work with its confidence scoring parameter? If I increase this, will it make it more stringent?
Last but not least, if I were to assemble my metagenome shotgun dataset into contigs, would it even be worth using Kraken2 if its still going to break the contigs into 31-32KMERS.