199-biotechnologies/claude-deep-research-skillGit

Claude deep research

Create research reports with citation checks, critical review and multiple export formats.

Before you start

Inputs: Research question, source scope and output requirements

Check the original documentation for supported AI tools, models and runtime dependencies.
Open the repository and follow the author’s installation instructions. Model APIs or external services may require separate accounts.
Try your own material, then review the facts, layout and output files.

Read the original installation guide ↗

License: Not specified. Check the repository’s usage terms.

Source snapshot: 2026-09-15. README ↗

Try a task like this

Use Claude deep research with my own source material. Confirm the required inputs and available tools, then produce an editable result.

Deep Research Skill for Claude Code

Enterprise-grade research engine for Claude Code. Produces citation-backed reports with source credibility scoring, multi-provider search, and automated validation.

Installation

# Clone into Claude Code skills directory
git clone https://github.com/199-biotechnologies/claude-deep-research-skill.git ~/.claude/skills/deep-research

No additional dependencies required for basic usage.

Optional: search-cli (multi-provider search)

For aggregated search across Brave, Serper, Exa, Jina, and Firecrawl:

brew tap 199-biotechnologies/tap && brew install search-cli
search config set keys.brave YOUR_KEY  # configure at least one provider

Usage

deep research on the current state of quantum computing

deep research in ultradeep mode: compare PostgreSQL vs Supabase for our stack

Research Modes

Mode	Phases	Duration	Best For
Quick	3	2-5 min	Initial exploration
Standard	6	5-10 min	Most research questions
Deep	8	10-20 min	Complex topics, critical decisions
UltraDeep	8+	20-45 min	Comprehensive reports, maximum rigor

Pipeline

Scope → Plan → Retrieve (parallel search + agents) → Triangulate → Outline Refinement → Synthesize → Critique (with loop-back) → Refine → Package

Key features:

Step 0: Retrieves current date before searches (prevents stale training-data year assumptions)
Parallel retrieval: 5-10 concurrent searches + 2-3 focused sub-agents returning structured evidence objects
First Finish Search: Adaptive quality thresholds by mode
Critique loop-back: Phase 6 can return to Phase 3 with delta-queries if critical gaps found
Multi-persona red teaming: Skeptical Practitioner, Adversarial Reviewer, Implementation Engineer (Deep/UltraDeep)
Disk-persisted citations: sources.json survives context compaction and continuation agents

Output

Reports saved to ~/Documents/[Topic]_Research_[Date]/:

Markdown (primary source of truth)
HTML (McKinsey-style, auto-opened in browser)
PDF (professional print via WeasyPrint)

Reports >18K words auto-continue via recursive agent spawning with context preservation.

Quality Standards

10+ sources, 3+ per major claim
Executive summary 200-400 words
Findings 600-2,000 words each, prose-first (>=80%)
Full bibliography with URLs, no placeholders
Automated validation: validate_report.py (9 checks) + verify_citations.py (DOI/URL/hallucination detection)
Validation loop: validate → fix → retry (max 3 cycles)

Search Tools

Tool	Priority	Setup
search-cli	Primary — all searches go here first	`brew install search-cli` + API keys
WebSearch	Fallback — if search-cli fails or rate-limited	None (built-in)
Exa MCP	Optional — semantic/neural search alongside search-cli	MCP config

Architecture

deep-research/
├── SKILL.md                          # Skill entry point (lean, ~100 lines)
├── reference/
│   ├── methodology.md                # 8-phase pipeline details
│   ├── report-assembly.md            # Progressive generation strategy
│   ├── quality-gates.md              # Validation standards
│   ├── html-generation.md            # McKinsey HTML conversion
│   ├── continuation.md               # Auto-continuation protocol
│   └── weasyprint_guidelines.md      # PDF generation
├── templates/
│   ├── report_template.md            # Report structure template
│   └── mckinsey_report_template.html # HTML report template
├── scripts/
│   ├── validate_report.py            # 9-check structure validator
│   ├── verify_citations.py           # DOI/URL/hallucination checker
│   ├── source_evaluator.py           # Source credibility scoring
│   ├── citation_manager.py           # Citation tracking
│   ├── md_to_html.py                 # Markdown to HTML converter
│   ├── verify_html.py                # HTML verification
│   └── research_engine.py            # Core orchestration engine
└── tests/
    └── fixtures/                     # Test report fixtures

Version History

Version	Date	Changes
2.3.1	2026-03-19	Template/validator harmonization, structured evidence, critique loop-back, multi-persona red teaming
2.3	2026-03-19	Contract harmonization, search-cli integration, dynamic year detection, disk-persisted citations, validation loops
2.2	2025-11-05	Auto-continuation system for unlimited length
2.1	2025-11-05	Progressive file assembly
1.0	2025-11-04	Initial release

License

MIT - modify as needed for your workflow.