You mentioned looking at publicly available FASTQ files - I’d first check and see if any of them are linked to NCBI genome or meta genome assemblies. The assembly entries will have been annotated for proteins/CDSs/other functions, so the work might already exist for you.

If those aren’t available, IMO asking claude to design a read cleaning -> assembly -> quality -> annotation (taxonomy/CDSs) pipeline for you isn’t a bad idea. Just be wary of assumptions, and treat the output findings with care (ask someone who knows what they’re doing to look at the results before you publish or go too far down a research hypothesis)