Hi,

First of all, thank you for all your work on EGAPx.
I'm curious about how EGAPx handles a previously soft-masked (lowercase) genome. Specifically:

1. Is it possible to bypass the masking step by telling EGAPx the genome is already masked (I don't think so, but want to double-check)?
2. Would feeding EGAPx with a masked genome cause any pipeline issues?
3. How does WindowMasker deal with a masked genome? Does it understand that the genome has been masked, or does it just ignore the lowercases and "double" mask it?
4. The final complete.genomic.fna in the output folder doesn't look masked. So, I would like to use my own soft-masked genome for NCBI submission. Would my masked.genomic.fna (used as input in EGAPx) match the EGAPx annotation output files (I think it would, but want to double-check)?

Thanks in advance,
Dani.