genome-toolkit

Universal genome data import supporting 23andMe v4/v5, AncestryDNA, MyHeritage, Nebula, and generic VCF. Also handles imputation prep and post-imputation import. Triggers on: /genome-import, "import my DNA data", "add raw file", "prepare for imputation", "import imputed data".

Goal-driven onboarding for new genome vault users. Triggers on: /genome-onboard, "set up my vault", "I just imported my data", "help me get started with my genome". Two modes: --quick (4 questions, fast vault bootstrap) or --full (22-question interview with validated psychological instruments, generates Profile Card + Action Plan).

Daily health tracking with genetic context: supplements, medications, symptoms, interventions, metrics. Use this skill whenever the user mentions taking supplements, logging symptoms, tracking health, reporting how they feel, or asks about their daily routine. Also triggers on: /genome-log, /log, "daily check-in", "track today", "I took my supplements", "feeling anxious", "my stomach hurts", "forgot my B12", "log symptoms", "how am I doing", "what did I take today". Even casual health mentions like "my nose is stuffed" or "had a rough night" should trigger this skill to offer logging.

Query Obsidian vault frontmatter with SQL-like syntax. Filter, sort, group, and aggregate notes by any frontmatter field. Replaces Dataview for CLI use. Triggers on: /genome-query, "query vault", "find notes", "list genes", "show protocols", "vault stats", "vault schema", "filter by".

Multi-agent validation pipeline for fact-checking claims, verifying evidence tiers, and ensuring prescriber document accuracy. Uses Codex CLI, NotebookLM, PubMed subagents, and Tavily search. Supports: audit (full vault), gene SYMBOL (single gene fact-check), protocol NAME (protocol/report fact-check). Triggers on: /genome-validate, "validate this note", "fact-check", "cross-check claims", "verify evidence", "audit this report", "fact-check gene X", "check protocol X".

Run analysis scripts: PRS, enrichment, vault audit, PubMed monitoring, consistency checks. Triggers on: /genome-analytics, "run PRS", "audit vault", "check PubMed", "run enrichment", "check consistency", "analyze pathway".

Create gene, system, or phenotype notes from SQLite genotype data and templates. Triggers on: /new-gene SYMBOL, /new-system NAME, "add gene X", "create system note", "create phenotype note for X".

Generate prescriber-facing reports and import biomarker lab results. Triggers on: /biomarker, /wallet-card, "import lab results", "analyze bloodwork", "generate prescriber summary", "create wallet card", "update PGx card".