option for reference sequence

[wbsimey]

I have tried many different ways to load the reference fasta file, but no luck. I tried no flag and get unrecognized command, I tried 'target' or 'reference' and get unrecognized command, I tried --target, I do not see any other flag to load the reference. I searched the help file and there is no 'reference' in the options. Please add some example commands. Thank you.