ranaalyan1/NGS-Agent ? reverse-engineered prompt

Build me a Python tool for wet lab NGS teams that helps with the annoying parts of analysis and monitoring.

I want a command line app that can watch a pipeline log in real time, spot common failure patterns, and explain them in plain English with a suggested fix. It should also be able to read a VCF and a QC summary file, then give a clean terminal report that highlights important variants, their likely significance, read depth, allele fraction, and any QC issues.

Add a demo mode that works right after install using bundled sample data, and make it easy to run a “doctor” style check that tells me whether my setup is ready. If possible, include an optional debate mode where multiple AI viewpoints review VUS variants and give a consensus summary, but keep the basic log watching and variant analysis working without any LLM setup.

Make it feel polished in the terminal, simple to install, and useful for people who are not bioinformatics experts.