# Deep Research

> Generate format-controlled research reports with evidence tracking, citations, and iterative review. This skill should be used when users request a research report, literature review, market or industry analysis, competitive landscape, policy or technical brief, or require a strict report template and section formatting that a single deepresearch pass cannot reliably enforce.

- Skill: `rongarede/deep-research` (Agent Skill, multi-file: 6 files)
- Install (CLI): `npx skillmds@latest add rongarede/deep-research`
- Raw SKILL.md: https://api.skillmd.com/api/skills/rongarede/deep-research/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Docs & Writing
- Author: rongarede (https://skillmd.com/u/rongarede)
- Updated: 2026-09-22
- Page: https://skillmd.com/skills/rongarede/deep-research

---


# Deep Research

Create high-fidelity research reports with strict format control, evidence mapping, and multi-pass synthesis.

## Quick Start

1. Clarify the report spec and format contract
2. Build a research plan and query set
3. Collect evidence with parallel agents (multi-source)
3.5. Download source PDFs (arXiv + sci-hub)
4. Triage sources and build an evidence table
4.5. Extract paragraphs from downloaded PDFs
5. Outline and section map
6. Multi-pass full drafting (parallel subagents)
7. UNION merge, enforce format compliance, verify citations
8. Evidence and citation verification
9. Present draft for human review and iterate

## Core Workflow

Copy this checklist and track progress:

```
Deep Research Progress:
- [ ] Step 1: Intake and format contract
- [ ] Step 2: Research plan and query set
- [ ] Step 3: Evidence collection (parallel agents)
- [ ] Step 3.5: PDF download (arXiv + sci-hub)
- [ ] Step 4: Source triage and evidence table
- [ ] Step 4.5: PDF paragraph extraction
- [ ] Step 5: Outline and section map
- [ ] Step 6: Multi-pass full drafting (parallel subagents)
- [ ] Step 7: UNION merge and format compliance
- [ ] Step 8: Evidence and citation verification
- [ ] Step 9: Present draft for human review and iterate
```

### Step 1: Intake and Format Contract

Establish the report requirements before any research:

- Confirm audience, purpose, scope, time range, and geography
- Lock output format: Markdown, DOCX, slides, or user-provided template
- Capture required sections and exact formatting rules
- Confirm citation style (footnotes, inline, numbered, APA, etc.)
- Confirm length targets per section
- Ask for any existing style guide or sample report

Create a concise report spec file:

```
Report Spec:
- Audience:
- Purpose:
- Scope:
- Time Range:
- Geography:
- Required Sections:
- Section Formatting Rules:
- Citation Style:
- Output Format:
- Length Targets:
- Tone:
- Must-Include Sources:
- Must-Exclude Topics:
```

If a user provides a template or an example report, treat it as a hard constraint and mirror the structure.

### Step 2: Research Plan and Query Set

Define the research strategy before calling tools:

- Break the main question into 3-7 subquestions
- Define key entities, keywords, and synonyms
- Identify primary sources vs secondary sources
- Define disqualifiers (outdated, low quality, opinion-only)
- Assemble a query set per section

Use [references/research_plan_checklist.md](references/research_plan_checklist.md) for guidance.

### Step 3: Evidence Collection (Deepresearch Tool)

Use the deepresearch tool to collect evidence and citations.

- Run multiple complete passes if coverage is uncertain
- Vary query phrasing to reduce blind spots
- Preserve raw tool output in files for traceability

#### Parallel Evidence Collection (Academic Research)

For academic literature searches, split evidence collection across multiple parallel agents by data source:

| Agent | Data Source | Tool |
|-------|-----------|------|
| Agent 1 | Semantic Scholar | semantic-scholar skill API |
| Agent 2 | arXiv preprints | arxiv-search skill + WebSearch site:arxiv.org |
| Agent 3 | IEEE/ACM + Chinese databases | WebSearch site:ieeexplore.ieee.org + Chinese keywords |

**Execution rules:**
- Launch all agents simultaneously with `run_in_background=true`
- Each agent writes to a separate raw output file (e.g., `raw_S2.md`, `raw_arXiv.md`, `raw_IEEE.md`)
- After all agents complete, merge raw files using UNION (Step 4)
- Never run a single agent for all dimensions when parallel execution is possible

**File structure (recommended):**
```
<output_dir>/research/<topic-name>/
  deepresearch_pass1.md
  deepresearch_pass2.md
  deepresearch_pass3.md
```

If deepresearch is unavailable, rely on user-provided sources only and state limitations explicitly.

### Step 3.5: PDF Download (Academic Research)

After evidence collection, download source PDFs for full-text extraction:

**Download routes (in priority order):**

| Source Type | Download Method | Tool |
|------------|----------------|------|
| arXiv papers | Direct curl: `https://arxiv.org/pdf/{id}.pdf` | Bash with proxy |
| DOI papers | sci-hub-download skill (OA → Sci-Hub → publisher) | sci-hub-download skill |
| Chinese papers | Manual download required | Flag for user |

**Execution:**
- Extract arXiv IDs and DOIs from evidence collection outputs using Grep
- Launch 2 parallel download agents: one for arXiv (curl), one for DOI (sci-hub)
- Save all PDFs to `<output_dir>/research/papers/`
- Create `download_log.md` with success/failure tracking
- Validate downloads: PDF files must be >100KB to be considered valid

**File structure:**
```
<output_dir>/research/papers/
  paper1.pdf
  paper2.pdf
  ...
  download_log.md
```

This step is MANDATORY for academic research tasks. Do not skip to Step 4 without downloading available PDFs.

### Step 4: Source Triage and Evidence Table

Normalize and score sources before drafting:

- De-duplicate sources across passes
- Score sources using [references/source_quality_rubric.md](references/source_quality_rubric.md)
- Build an evidence table mapping claims to sources

Evidence table minimum columns:

- Source ID
- Title
- Publisher
- Date
- URL or reference
- Quality tier (A/B/C)
- Notes

### Step 4.5: PDF Paragraph Extraction (Academic Research)

Read downloaded PDFs and extract paragraphs matching research keywords:

**Execution:**
- Split PDFs into batches of ~10 by filename alphabetical order
- Launch parallel reader agents (one per batch) with `run_in_background=true`
- Each reader uses the Read tool with `pages` parameter to read PDFs in 20-page chunks
- Search for keyword matches: extract the full surrounding paragraph (at least 3 sentences of context)
- Record: page number, section heading, full paragraph text

**Output format per paper:**
```
### [filename] Paper Title
#### Page X — Section Heading
> Extracted paragraph text...
```

**Write extracted paragraphs to:**
```
<output_dir>/research/extracts/
  batch1.md
  batch2.md
  ...
```

These raw extracts feed into Step 5 (outline) and Step 6 (drafting) as primary evidence.

### Step 5: Outline and Section Map

Create an outline that enforces the format contract:

- Use the template in [references/research_report_template.md](references/research_report_template.md)
- Produce a section map with required elements per section
- Confirm ordering and headings match the report spec

### Step 6: Multi-Pass Full Drafting (Parallel Subagents)

Avoid single-pass drafting; generate multiple complete reports, then merge.

#### Preferred Strategy: Parallel Subagents (Complete Draft Each)

Use the Task tool to spawn parallel subagents with isolated context. Each subagent must:

- Load the report spec, outline, and evidence table
- Draft the FULL report (all sections)
- Enforce formatting rules and citation style

**Implementation pattern:**
```
Task(subagent_type="general-purpose", prompt="Draft complete report ...", run_in_background=false) -> version1.md
Task(subagent_type="general-purpose", prompt="Draft complete report ...", run_in_background=false) -> version2.md
Task(subagent_type="general-purpose", prompt="Draft complete report ...", run_in_background=false) -> version3.md
```

**Write drafts to files, not conversation context:**
```
<output_dir>/intermediate/<topic-name>/version1.md
<output_dir>/intermediate/<topic-name>/version2.md
<output_dir>/intermediate/<topic-name>/version3.md
```

### Step 7: UNION Merge and Format Compliance

Merge using UNION, never remove content without evidence-based justification:

- Keep all unique findings from all versions
- Consolidate duplicates while preserving the most detailed phrasing
- Ensure every claim in the merged draft has a cited source
- Enforce the exact section order, headings, and formatting
- Re-run formatting rules from [references/formatting_rules.md](references/formatting_rules.md)

### Step 8: Evidence and Citation Verification

Verify traceability:

- Every numeric claim has at least one source
- Every recommendation references supporting evidence
- No orphan claims without citations
- Dates and time ranges are consistent
- Conflicts are explicitly called out with both sources

Use [references/completeness_review_checklist.md](references/completeness_review_checklist.md).

### Step 9: Present Draft for Human Review and Iterate

Present the draft as a reviewable version:

- Emphasize that format compliance and factual accuracy need human review
- Accept edits to format, structure, and scope
- If the user provides another AI output, cross-compare and UNION merge

## Output Requirements

- Match the requested language and tone
- Preserve technical terms in English
- Respect the report spec and formatting rules
- Include a references section or bibliography

## Reference Files

| File | When to Load |
| --- | --- |
| [research_report_template.md](references/research_report_template.md) | Build outline and draft structure |
| [formatting_rules.md](references/formatting_rules.md) | Enforce section formatting and citation rules |
| [source_quality_rubric.md](references/source_quality_rubric.md) | Score and triage sources |
| [research_plan_checklist.md](references/research_plan_checklist.md) | Build research plan and query set |
| [completeness_review_checklist.md](references/completeness_review_checklist.md) | Review for coverage, citations, and compliance |

## Anti-Patterns

- Single-pass drafting without parallel complete passes
- Splitting passes by section instead of full report drafts
- Ignoring the format contract or user template
- Claims without citations or evidence table mapping
- Mixing conflicting dates without calling out discrepancies
- Copying external AI output without verification
- Deleting intermediate drafts or raw research outputs
- Running a single search agent when multiple data sources are available
- Skipping PDF download and relying only on search snippets/abstracts
- Sequential evidence collection when parallel execution is possible
- Waiting for user prompts between steps instead of pipeline execution