We have some metagenomic shotgunning data that we assembled into contigs using SOAPdenovo. Now, we wanted to feed these contigs into Kraken2. However, I've looked over some literature, and it seems like most people feed the raw reads into Kraken2. Is there any advantage using contigs? Or because of the k-mer approach that Kraken2 uses, we are actually doing ourselves a disservice.
Secondly, if we don't use Kraken2 with our contigs, what are some options we can use with our assembled contigs?