Deep Research

This skill conducts comprehensive research on complex topics using a multi-agent architecture, producing detailed reports similar to academic journals or whitepapers.

Purpose

The deep-research skill transforms broad research questions into thorough, well-cited reports using a three-agent system:

1. Lead Agent (You): Conducts interviews, plans research, orchestrates subagents
2. Researcher Agents: Execute web searches and save findings to files
3. Report-Writer Agent: Synthesizes research notes into final report

When to Use This Skill

Use this skill when the user requests:

• In-depth research on a complex topic
• A comprehensive report or analysis
• Research that requires multiple sources and synthesis
• Deep investigation similar to academic or whitepaper standards
• Detailed analysis with proper citations

Do NOT use this skill for:

• Simple fact-finding queries
• Single-source information lookup
• Code-only research within repositories
• Quick exploratory searches

Agent Architecture

Lead Agent (You - the Orchestrator)

Role: Interview user, plan research threads, spawn and coordinate subagents

Tools allowed: Task (to spawn subagents), AskUserQuestion, Write (for research plan only)

Responsibilities:

• Conduct user interview to scope research
• Perform initial reconnaissance
• Decompose topic into 10+ research threads
• Spawn researcher agents in parallel
• Spawn report-writer agent after research completes

Researcher Agents

Role: Execute focused research on assigned subtopic

Tools allowed: WebSearch, WebFetch, Write

Responsibilities:

• Search the web for information on assigned topic
• Fetch and analyze relevant pages
• Save structured research notes to research_notes/ directory

Output format: Each researcher saves a markdown file to research_notes/[subtopic-slug].md with:

• Summary of findings
• Key facts and data points
• Source URLs with brief descriptions
• Notable quotes or excerpts
• Conflicts or gaps identified

Report-Writer Agent

Role: Synthesize all research notes into final report

Tools allowed: Read, Glob, Write

Responsibilities:

• Read all files from research_notes/ directory
• Identify themes, patterns, and conflicts across sources
• Structure and write the final report
• Create the sources bibliography

Research Process

Phase 1: Interview and Scope Definition

Start by interviewing the user to understand their research needs. Ask questions about:

1. Research objectives: What are they trying to understand or decide?
2. Depth and breadth: How comprehensive should the research be?
3. Target audience: Who will read this report?
4. Key questions: What specific questions need answering?
5. Time constraints: Is this time-sensitive information?
6. Scope boundaries: What should be explicitly included or excluded?

The interview should be thorough but efficient. Use the AskUserQuestion tool to gather this information in 2-3 rounds of questions maximum.

Phase 2: Initial Reconnaissance

After the interview, perform initial reconnaissance to identify the research landscape:

1. Conduct 3-5 broad web searches to map the topic space
2. Identify key subtopics, domains, and areas of focus
3. Note promising sources, authoritative voices, and research gaps
4. Create a research plan outlining 10+ specific research threads

Save the research plan to research_plan.md documenting:

• The research threads identified
• Which researcher will handle each thread
• Expected output from each researcher

Phase 3: Parallel Research (Researcher Agents)

Launch 10+ researcher agents in parallel using the Task tool. Each agent receives a focused research assignment.

Spawning researcher agents:

Task tool with:
- subagent_type: "general-purpose"
- prompt: Include these elements:
  1. Clear statement: "You are a RESEARCHER agent"
  2. Specific subtopic assignment
  3. Tool restrictions: "Only use WebSearch, WebFetch, and Write tools"
  4. Output instructions: "Save your findings to research_notes/[subtopic].md"
  5. Format requirements for the research notes file

Example researcher prompt:

You are a RESEARCHER agent investigating: "Technical implementation of quantum error correction"

YOUR TOOLS: Only use WebSearch, WebFetch, and Write.

TASK:
1. Use WebSearch to find authoritative sources on quantum error correction implementation
2. Use WebFetch to extract detailed information from promising sources
3. Save your findings to research_notes/quantum-error-correction.md

OUTPUT FORMAT (save to research_notes/quantum-error-correction.md):
# Quantum Error Correction Implementation

## Summary
[2-3 paragraph summary of key findings]

## Key Findings
- [Bullet points of important facts, data, techniques]

## Sources
1. [URL] - [Brief description of what this source contributed]
2. [URL] - [Brief description]
...

## Notable Quotes
> "[Relevant quote]" - Source

## Gaps and Conflicts
- [Any conflicting information or areas needing more research]

Launch all researcher agents in a single message with multiple Task tool calls for true parallelism.

Phase 4: Report Generation (Report-Writer Agent)

After all researcher agents complete, spawn a single report-writer agent:

Spawning the report-writer agent:

Task tool with:
- subagent_type: "general-purpose"
- prompt: Include these elements:
  1. Clear statement: "You are a REPORT-WRITER agent"
  2. Tool restrictions: "Only use Read, Glob, and Write tools"
  3. Instructions to read all files from research_notes/
  4. Report structure requirements
  5. Output file paths for report and sources

Example report-writer prompt:

You are a REPORT-WRITER agent synthesizing research findings into a final report.

YOUR TOOLS: Only use Read, Glob, and Write.

TASK:
1. Use Glob to list all files in research_notes/
2. Use Read to load each research notes file
3. Synthesize findings into a comprehensive report
4. Write the final report to [topic]-report.md
5. Write the sources bibliography to [topic]-sources.md

REPORT STRUCTURE:
- Executive Summary (2-3 paragraphs)
- [Adaptive middle sections based on topic]
- Critical Analysis
- Conclusions
- References (numbered citations)

SOURCES FILE STRUCTURE:
# Research Sources for [Topic]

## [1] Source Title
- **URL**: [url]
- **Accessed**: [date]
- **Type**: [Academic paper / Blog post / Documentation / News article]
- **Key Points**: [bullet points]
- **Relevance**: [why this source matters]

WRITING GUIDELINES:
- Use numbered citations [1], [2], etc.
- Cross-reference findings across multiple researcher notes
- Note any conflicts or gaps in the research
- Use clear, precise academic language
- Include tables for comparisons where appropriate

Phase 5: Output and Summary

After the report-writer completes:

1. Inform the user of the generated files:

   • [topic]-report.md: Main research report
   • [topic]-sources.md: Complete bibliography
   • research_notes/: Directory of raw research (can be deleted)

2. Provide a brief verbal summary of key findings

3. Offer to answer follow-up questions or expand on any section

File Structure

./
├── research_plan.md           # Your research plan (Phase 2)
├── research_notes/            # Researcher agent outputs (Phase 3)
│   ├── subtopic-1.md
│   ├── subtopic-2.md
│   └── ...
├── [topic]-report.md          # Final report (Phase 4)
└── [topic]-sources.md         # Bibliography (Phase 4)

Logging and Observability

Track research progress by documenting in research_plan.md:

1. Research threads assigned: List each subtopic and its researcher
2. Status tracking: Note when each researcher completes
3. Issues encountered: Document any gaps or conflicts found

This provides transparency into the research process and helps with debugging or expanding research later.

Best Practices

Agent Separation

• Lead agent: ONLY spawns agents and coordinates - no direct research
• Researchers: ONLY search, fetch, and write notes - no synthesis
• Report-writer: ONLY reads notes and writes report - no new research

This separation ensures clean handoffs and reproducible results.

Research Quality

• Prioritize authoritative, recent sources (especially for time-sensitive topics)
• Cross-reference claims across multiple researcher notes
• Note conflicting information or perspectives
• Distinguish between facts, expert opinions, and speculation
• Be transparent about limitations in available information

Efficiency

• Launch all researcher agents truly in parallel (single message, multiple Task tool calls)
• Use model="haiku" for researcher agents to reduce costs
• Use model="sonnet" for report-writer agent for better synthesis
• Clear task delineation prevents redundant research

Common Patterns

Comparative Research

When comparing technologies, approaches, or solutions:

• Assign one researcher per option being compared
• Assign one researcher for cross-cutting concerns (performance, cost, etc.)
• Report-writer creates comparison tables

Technical Deep-Dives

When researching technical topics:

• Assign researchers to: fundamentals, implementation, case studies, limitations
• Report-writer structures from basics to advanced

Market/Landscape Research

When surveying a domain or market:

• Assign researchers to: major players, emerging players, trends, analysis firms
• Report-writer categorizes and evaluates the landscape

Historical/Evolution Research

When investigating how something developed:

• Assign researchers to different time periods or key events
• Report-writer creates timeline and connects to present