Using anonym vs. other_pt for -F flag

[Homap]

Hello,

Thanks so much for the amazing tool!

My question is about using the -F flag for assembling algal cpDNA. I ran get_organelle_from_reads.py with -F other_pt and -F anonym. In both cases, I provided the program with a reference fasta in -s and a gene set for --genes. In both cases, when I check the seed directory, I see that the reference genome I have provided is being indexed for bowtie.

I was wondering if there is any difference between using the two -F flags (anonym vs. other_pt) when I am providing my own reference and gene set?

Thank you!