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:

• Lead Agent (You): Conducts interviews, plans research, orchestrates subagents

• Researcher Agents: Execute web searches and save findings to files

• 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:

• Research objectives: What are they trying to understand or decide?

• Depth and breadth: How comprehensive should the research be?

• Target audience: Who will read this report?

• Key questions: What specific questions need answering?

• Time constraints: Is this time-sensitive information?

• 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:

• Conduct 3-5 broad web searches to map the topic space

• Identify key subtopics, domains, and areas of focus

• Note promising sources, authoritative voices, and research gaps

• 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:

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)

Provide a brief verbal summary of key findings

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 :

• Research threads assigned: List each subtopic and its researcher

• Status tracking: Note when each researcher completes

• 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