Claude Code Deep Research Agent

A sophisticated multi-agent research framework that implements OpenAI's Deep Research and Google Gemini's Deep Research capabilities using Claude Code's native features.

Overview

This project leverages Claude Code's Skills and Commands system to conduct comprehensive, citation-backed research through:

Graph of Thoughts (GoT) Framework - Intelligent research path management with graph-based reasoning
7-Phase Deep Research Process - Structured methodology for quality research
Multi-Agent Architecture - Parallel research agents with specialized roles
Citation Validation System - A-E source quality ratings with chain-of-verification

Quick Start

Prerequisites

Claude Code CLI installed
Active Claude Code account with API access

Installation

Clone this repository:

git clone <repository-url>
cd Claude-Code-Deep-Research-main

The Skills and Commands are already configured in .claude/ directory

Basic Usage

The simplest way to conduct deep research:

/deep-research [your research topic]

Example:

/deep-research AI applications in clinical diagnosis

This single command will:

Ask clarifying questions to refine your research needs
Create a structured research plan
Deploy multiple parallel research agents
Synthesize findings into a comprehensive report
Validate all citations
Output results to RESEARCH/[topic]/ directory

Advanced Usage

Step-by-Step Research Workflow

For more control over the research process:

1. Refine Your Question

/refine-question Should I use WebAssembly for my project?

The Question Refiner will ask 5-6 clarifying questions about:

Specific focus areas
Output format requirements
Geographic and time scope
Target audience
Special requirements

2. Plan Research (Optional)

/plan-research [structured prompt from step 1]

Creates a detailed execution plan showing:

How the topic breaks into subtopics
Which agents will be deployed
Expected timeline

3. Execute Research

/deep-research [your topic]

4. Synthesize Findings (If needed)

/synthesize-findings RESEARCH/[topic]/research_notes/

5. Validate Citations

/validate-citations RESEARCH/[topic]/full_report.md

Project Structure

claude-code-deep-research/
├── .claude/
│   ├── skills/                    # Research skills
│   │   ├── question-refiner/      # Question refinement
│   │   ├── research-executor/     # Main research execution
│   │   ├── got-controller/        # Graph of Thoughts controller
│   │   ├── citation-validator/    # Citation validation
│   │   └── synthesizer/           # Research synthesis
│   ├── commands/                  # User commands
│   │   ├── deep-research.md       # Main research command
│   │   ├── refine-question.md     # Question refinement
│   │   ├── plan-research.md       # Research planning
│   │   ├── synthesize-findings.md # Findings synthesis
│   │   └── validate-citations.md  # Citation validation
│   └── settings.local.json        # Tool permissions
├── RESEARCH/                      # Research outputs
│   └── [topic_name]/
│       ├── README.md
│       ├── executive_summary.md
│       ├── full_report.md
│       ├── data/
│       ├── visuals/
│       ├── sources/
│       ├── research_notes/
│       └── appendices/
├── CLAUDE.md                      # Quick reference for Claude Code
├── CLAUDE2.md                     # Graph of Thoughts guide
├── PROJECT_UNDERSTANDING.md       # Architecture documentation
├── IMPLEMENTATION_GUIDE.md        # User guide with examples
└── README.md                      # This file

Research Output Structure

Each research project creates a structured output:

RESEARCH/[topic_name]/
├── README.md                    # Overview and navigation
├── executive_summary.md         # 1-2 page key findings
├── full_report.md               # Complete analysis (20-50 pages)
├── data/
│   └── statistics.md            # Key numbers and facts
├── visuals/
│   └── descriptions.md          # Chart/graph descriptions
├── sources/
│   ├── bibliography.md          # Complete citations
│   └── source_quality_table.md  # A-E quality ratings
├── research_notes/
│   └── agent_findings_summary.md # Raw agent outputs
└── appendices/
    ├── methodology.md           # Research methods
    └── limitations.md           # Unknowns and gaps

Citation Requirements

Every factual claim includes:

Author/Organization name
Publication date
Source title
Direct URL/DOI
Page numbers (if applicable)

Source Quality Ratings:

A: Peer-reviewed RCTs, systematic reviews, meta-analyses
B: Cohort studies, clinical guidelines, reputable analysts
C: Expert opinion, case reports, mechanistic studies
D: Preprints, preliminary research, blogs
E: Anecdotal, theoretical, speculative

Graph of Thoughts Framework

The GoT framework manages research as a graph with these operations:

| Operation | Purpose | Example | |-----------|---------|---------| | Generate(k) | Spawn k parallel research paths | Generate(4) from root → 4 research paths | | Aggregate(k) | Merge k findings into synthesis | Aggregate(3) → 1 comprehensive report | | Refine(1) | Improve existing finding | Refine(node_5) → Enhanced quality | | Score | Rate quality (0-10) | Score based on citations, accuracy | | KeepBestN(n) | Prune to top n nodes | KeepBestN(3) → Retain best 3 |

Research Patterns:

Balanced: Generate(4-5) → Score best → Deepen top → Aggregate
Depth-first: Generate(3) → Take best → Generate(3) from it
Breadth-first: Generate(8) → KeepBestN(5) → Generate(2) each

Documentation

| Document | Description | |----------|-------------| | CLAUDE.md | Quick reference for Claude Code instances | | CLAUDE2.md | Complete Graph of Thoughts implementation | | PROJECT_UNDERSTANDING.md | Detailed architecture and design | | IMPLEMENTATION_GUIDE.md | User guide with examples and workflows |

Commands Reference

| Command | Usage | Description | |---------|-------|-------------| | /deep-research | /deep-research [topic] | Execute complete research workflow | | /refine-question | /refine-question [question] | Refine into structured prompt | | /plan-research | /plan-research [prompt] | Create execution plan | | /synthesize-findings | /synthesize-findings [dir] | Combine research outputs | | /validate-citations | /validate-citations [file] | Verify citation quality |

Examples

Market Research

/deep-research AI in healthcare market, focus on clinical diagnosis,
             comprehensive report, global scope, 2022-2024 data,
             audience is healthcare executives

Technical Assessment

/deep-research WebAssembly vs JavaScript performance benchmarks

Academic Literature Review

/deep-research Transformer architectures in AI,
             peer-reviewed sources only, 2017-present,
             comprehensive literature review

Features

Multi-agent parallel research (3-8 agents simultaneously)
Graph of Thoughts optimization for quality
Automatic citation validation
Source quality ratings (A-E scale)
Chain-of-verification to prevent hallucinations
Structured output with executive summaries
Cross-source triangulation

Performance

Quick research (narrow topic): 10-15 minutes
Standard research (moderate scope): 20-30 minutes
Comprehensive research (broad scope): 30-60 minutes
Academic literature review: 45-90 minutes

Contributing

Contributions are welcome! To add new skills or improvements:

Follow the skill structure in .claude/skills/
Include SKILL.md, instructions.md, examples.md
Test with diverse research topics
Update documentation

License

This project is provided as-is for educational and research purposes.

Acknowledgments

Graph of Thoughts framework inspired by SPCL, ETH Zürich
Built with Claude Code
7-Phase Research Process based on deep research best practices

For detailed usage instructions, see IMPLEMENTATION_GUIDE.md

For architecture details, see PROJECT_UNDERSTANDING.md

Claude-Code-Deep-Research-main

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