Hello @Nondumiso_L_Ntuli,
The --o-reference-genomes, according to the command line help text, are either:
- the reference sequences that the QUAST software downloads if you don't provide an input to
--i-references, or - the reference sequences you provided to
--i-references
So in your case it sounds like it would be the former. I'm not very familiar with QUAST but I believe what is happening is that it queries some database with each contig, downloads a reference genome that the database considers the best match, and then aligns one or more contigs to the reference genome. Hopefully this clears up the confusion.