deep-research

Category: Data & AI | Uploader: 199-biotechnologies | Downloads: 0 | Version: v1.0（Latest）

Conducts enterprise-grade research with multi-source synthesis, citation tracking, and verification. Produces citation-backed reports through a structured pipeline with source credibility scoring. Triggers on "deep research", "comprehensive analysis", "research report", "compare X vs Y", "analyze trends", or "state of the art". Not for simple lookups, debugging, or questions answerable with 1-2 searches.

Changelog: Source: GitHub https://github.com/199-biotechnologies/claude-deep-research-skill

Directory Structure

Current level: Root

📁 reference/
- 📄 continuation.md 4.4 KB
- 📄 html-generation.md 2.9 KB
- 📄 methodology.md 15.7 KB
- 📄 quality-gates.md 5.5 KB
- 📄 report-assembly.md 3.3 KB
- 📄 weasyprint_guidelines.md 5.7 KB
📁 scripts/
- 📄 citation_manager.py 5.9 KB
- 📄 md_to_html.py 9.7 KB
- 📄 research_engine.py 16.1 KB
- 📄 source_evaluator.py 9.3 KB
- 📄 validate_report.py 12.1 KB
- 📄 verify_citations.py 15.1 KB
- 📄 verify_html.py 7.6 KB
📁 templates/
- 📄 mckinsey_report_template.html 10.2 KB
- 📄 report_template.md 12.8 KB
📁 tests/
- 📁 fixtures/
  - 📄 invalid_report.md 288 B
  - 📄 valid_report.md 3.3 KB
📄 .gitignore 248 B
📄 README.md 4.7 KB
📄 requirements.txt 579 B
📄 SKILL.md 3.6 KB

SKILL.md

---
name: deep-research
description: Conducts enterprise-grade research with multi-source synthesis, citation tracking, and verification. Produces citation-backed reports through a structured pipeline with source credibility scoring. Triggers on "deep research", "comprehensive analysis", "research report", "compare X vs Y", "analyze trends", or "state of the art". Not for simple lookups, debugging, or questions answerable with 1-2 searches.
---

# Deep Research

## Core Purpose

Deliver citation-backed, verified research reports through a structured pipeline with source credibility scoring, evidence persistence, and progressive context management.

**Autonomy Principle:** Operate independently. Infer assumptions from context. Only stop for critical errors or incomprehensible queries.

---

## Decision Tree

```
Request Analysis
+-- Simple lookup? --> STOP: Use WebSearch
+-- Debugging? --> STOP: Use standard tools
+-- Complex analysis needed? --> CONTINUE

Mode Selection
+-- Initial exploration --> quick (3 phases, 2-5 min)
+-- Standard research --> standard (6 phases, 5-10 min) [DEFAULT]
+-- Critical decision --> deep (8 phases, 10-20 min)
+-- Comprehensive review --> ultradeep (8+ phases, 20-45 min)
```

**Default assumptions:** Technical query = technical audience. Comparison = balanced perspective. Trend = recent 1-2 years.

---

## Workflow Overview

| Phase | Name | Quick | Standard | Deep | UltraDeep |
|-------|------|-------|----------|------|-----------|
| 1 | SCOPE | Y | Y | Y | Y |
| 2 | PLAN | - | Y | Y | Y |
| 3 | RETRIEVE | Y | Y | Y | Y |
| 4 | TRIANGULATE | - | Y | Y | Y |
| 4.5 | OUTLINE REFINEMENT | - | Y | Y | Y |
| 5 | SYNTHESIZE | - | Y | Y | Y |
| 6 | CRITIQUE | - | - | Y | Y |
| 7 | REFINE | - | - | Y | Y |
| 8 | PACKAGE | Y | Y | Y | Y |

---

## Execution

**On invocation, load relevant reference files:**

1. **Phase 1-7:** Load [methodology.md](./reference/methodology.md) for detailed phase instructions
2. **Phase 8 (Report):** Load [report-assembly.md](./reference/report-assembly.md) for progressive generation
3. **HTML/PDF output:** Load [html-generation.md](./reference/html-generation.md)
4. **Quality checks:** Load [quality-gates.md](./reference/quality-gates.md)
5. **Long reports (>18K words):** Load [continuation.md](./reference/continuation.md)

**Templates:**
- Report structure: [report_template.md](./templates/report_template.md)
- HTML styling: [mckinsey_report_template.html](./templates/mckinsey_report_template.html)

**Scripts:**
- `python scripts/validate_report.py --report [path]`
- `python scripts/verify_citations.py --report [path]`
- `python scripts/md_to_html.py [markdown_path]`

---

## Output Contract

**Required sections:**
- Executive Summary (200-400 words)
- Introduction (scope, methodology, assumptions)
- Main Analysis (4-8 findings, 600-2,000 words each, cited)
- Synthesis & Insights (patterns, implications)
- Limitations & Caveats
- Recommendations
- Bibliography (COMPLETE - every citation, no placeholders)
- Methodology Appendix

**Output files (all to `~/Documents/[Topic]_Research_[YYYYMMDD]/`):**
- Markdown (primary source)
- HTML (McKinsey style, auto-opened)
- PDF (professional print, auto-opened)

**Quality standards:**
- 10+ sources, 3+ per major claim
- All claims cited immediately [N]
- No placeholders, no fabricated citations
- Prose-first (>=80%), bullets sparingly

---

## When to Use / NOT Use

**Use:** Comprehensive analysis, technology comparisons, state-of-the-art reviews, multi-perspective investigation, market analysis.

**Do NOT use:** Simple lookups, debugging, 1-2 search answers, quick time-sensitive queries.

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deep-research

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SKILL.md

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