I have metagenomic data so I am using kraken2 which processed my reads and mapped them against various databases to see what species I have. This is great and what I wanted.
But, I need to compare the results using metaSPADES, but all I can find in metaSPADES is how to get the contigs.fasta file which I understand is my main output file. What is the next step? Do I simply BLAST these contigs (which would take sooo long because there are millions of contigs)? I think I should remap my reads against the contigs to get coverage but how do I get taxonomy information? Does metaSPADES have a builtin database like kraken2 does that I am just somehow missing here (I don't see any flags or options when using the help function).
Any tips on this would be great!