Overview
Skills are what turn the agent from a tool-caller into a clinical-genetics colleague—they are the key to making Noxia work smoothly with AI.
Why Skills matter
The MCP connection gives the agent Noxia’s tools and data: it can upload a VCF, trigger annotation, pull evidence. But tools alone don’t know the clinical playbook—which checks come first, what evidence to weigh, how to apply ACMG, when a result is good enough to stop. Skills supply exactly that. Each Skill is a packaged set of clinical procedures and judgment that the agent loads on demand, so it sequences a case the way an experienced geneticist would.
Skills also carry built-in safety floors. They won’t re-annotate a case that’s already ready, won’t inflate a variant beyond its evidence, accept VUS and negative results as valid outcomes, and require your manual approval before anything is submitted.
The workflow, skill by skill
The Skills mirror the clinical workflow. A typical case moves through three core Skills in order:
- noxia-case-management — Creates the case, uploads the VCF, triggers annotation, and sets the HPO phenotype terms. This is where every analysis begins.
- noxia-variant-analysis — Runs quality-control review, scans for candidate variants driven by the case’s phenotype, and performs ACMG screening to rank what’s worth a closer look.
- noxia-reporting — Classifies the chosen variants, marks findings for the report, and drafts the report fields for your review.
Three more Skills come in where a case needs them:
- noxia-variant-classifier — Deep ACMG/VCEP classification backed by ClinGen gene-specific guidelines (28-criterion analysis across 100+ genes, with optional literature retrieval). Insert it between analysis and reporting when a variant is hard to call.
- noxia-phenotype-inference — For negative WES results, reasons from the HPO phenotype to infer assay-blind mechanisms—CNV, uniparental disomy (UPD), imprinting, repeat expansions, mitochondrial DNA—that a standard SNV/indel scan would miss.
- noxia-fast-forward — Runs the whole pipeline end to end in a single unattended pass, for when you want one-shot analysis and a draft report.
Skill reference
| Skill | What it does |
|---|---|
| noxia-case-management | Case creation, VCF upload, annotation, HPO terms |
| noxia-variant-analysis | QC review, phenotype-driven candidate scan, ACMG screening |
| noxia-reporting | Variant classification, finding selection, report drafting |
| noxia-variant-classifier | Deep ACMG/VCEP classification with ClinGen gene-specific guidelines |
| noxia-phenotype-inference | Mechanism inference for negative WES (CNV, UPD, imprinting, repeats, mtDNA) |
| noxia-fast-forward | End-to-end unattended analysis and reporting in one pass |
Installing the Skills
All six Skills install in one step. From your project root:
npx skills add muwenbo/noxia-skills -a claude-codeThis drops them into .claude/skills/, where Claude Code discovers them automatically. The full walkthrough—including the Node.js prerequisite—is in step 4 of Installation & setup. The noxia-variant-classifier Skill additionally needs Python 3.7+ with the requests and beautifulsoup4 packages for its literature retrieval.