I'm working with whole genome metagenomic samples from human skin, and I'm using MEGAHIT for assembly and MetaQuast for evaluation. However, MetaQuast requires a list of reference genomes for the analysis (if I understood correctly). When I perform the evaluation without the references, it uses BLASTN for aligning contigs to SILVA 16S rRNA database. Since I'm working with whole genome sequences, this is not an optimal choice. As expected, MetaQuast is identifying only two species in my contigs file, although I have manually checked through BLASTN that there are contigs that match other species' genomes. And this evaluation makes my assembly looks terrible. Since I'm working with samples from human skin, it wouldn't be viable to download a database of reference genomes and perform MetaQuast using a local alignment. So, what would be the best approach to perform the evaluation correctly in my case?
Looking forward to discussing it!