Using multiple reference genomes for alignment in dorado?

Question

[gideonav]

The samples I have sequenced are a mixed culture of three known species. I know you can align in-line with the dorado basecaller and upload a reference, but is there a way to use multiple reference genomes for alignment?

Answer 1

[GenoMax]

You can cat the references together and use as one. Just make sure the fasta headers are unique.