wes-clinical-report-en
Generates professional clinical PDF reports in English from WES (Whole Exome Sequencing) data with clinical interpretation summary, pharmacogenomic alerts, and follow-up recommendations.
npx skills add BioTender-max/awesome-bio-agent-skills --skill wes-clinical-report-en --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# WES Clinical Report (English) Skill for generating professional clinical PDF reports in English from whole exome sequencing (WES) data. Designed for Novogene WES data (GATK + ANNOVAR pipeline) but adaptable to any WES pipeline with equivalent annotations. ## Trigger **Fire this skill when the user says any of:** - "generate WES clinical report in English" - "English exome PDF report" - "WES report PDF" - "clinical report from exome data" - "Novogene report English" - "exome clinical PDF" **Do NOT fire when:** - User asks for a Spanish report (use `wes-clinical-report-es`) - User asks for variant annotation only (use `variant-annotation`) - User asks for ACMG classification only (use `clinical-variant-reporter`) ## Scope One skill, one task: convert WES markdown reports into professional English-language clinical PDFs with interpretation. ## Workflow 1. Parse WES markdown report (structured sections 1-7) 2. Extract KPI metrics from Exome Summary 3. Extract pathogenic variants, PGx alerts, rare damaging variants 4. Build interpretive summary paragraph 5. Render all sections as styled PDF with clinical tables 6. Add ancestry estimation (section 8) if data available 7. Add limitation
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Generate reports for all samples python skills/wes-clinical-report-en/wes_clinical_report_en.py \ Generate report for a single sample Demo with default Novogene data python skills/wes-clinical-report-en/wes_clinical_report_en.py --demo
What does the wes-clinical-report-en skill do?
Generates professional clinical PDF reports in English from WES (Whole Exome Sequencing) data with clinical interpretation summary, pharmacogenomic alerts, and follow-up recommendations.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill wes-clinical-report-en --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.