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I'm not in bioinformatics and don't do string processing, so I can't really help too much here.
I'd really urge you to come ask this on the julia Discourse Forum or Zulip and I promise you'll get high quality useful responses from people who understand your needs better than I.
> How do I find substrings & replace them efficiently? How do you split a string with delimiters? Regular Expressions?
This is something that the BioJulia people have put a lot of work into. Yes, you can use regular expressions, but they've managed to squeeze a lot of performance out of more specialized approaches, e.g.
https://github.com/BioJulia/Automa.jl
https://github.com/jakobnissen/ScanByte.jl
But for more straightforward usage, julia has the `findfirst` function which can search for occurrences of a substring, `replace` which can do replacements either with a literal pattern or a regex, and `split` which can split a string with delimiters.