4 Conclusion

The microbiONT package represents a paradigm shift towards accessible, educational, and privacy-centric bioinformatics. By synergizing established CLI tools with an intuitive graphical interface and a local AI module, the platform effectively dismantles the technical barriers associated with Nanopore data analysis. This design empowers microbiologists to not only perform comprehensive 16S/18S analysis independently but also to cultivate bioinformatics expertise through AI-assisted guidance. Crucially, this accessibility does not come at the cost of precision; our benchmarking demonstrates that microbiONT yields a more accurate taxonomic profile than the standard EPI2ME workflow, characterized by a marked reduction in unclassified reads and enhanced genus-level resolution. Ultimately, driven by AI-guided support, local processing, and analytical rigor, microbiONT transforms 16S/18S data analysis from a specialized bottleneck into a convenient, routine practice for every laboratory.