deep-research

What the source does

• FilesystemNone observedNo reads or writes in the source
• NetworkDeclared2 observations
• ShellNone observedNo commands run in the source
• DependenciesPinnedNothing floats
• SecretsNone foundNo keys in source

Five audit layers

Gates applied: no behavioural pass, no license.

Audit 0.4.1 · source sha d875b0736241 · 20 Oct 2026Report an issue or request a re-scan

• Publisher199-biotechnologies GitHub organizationOwner of the repository this skill is read from
• Source folder199-biotechnologies/claude-deep-research-skillThe exact folder we audited
• LicenceNot declaredAs the repository states it
• Commit pinned for this verdictd875b0736241A new audit runs when the source changes
• Repository statusNot archivedLast push 191 days ago
• Sandboxed runNot runSkills are read, not executed; layer L4 is skipped

Its description: Use when the user needs multi-source research with citation tracking, evidence persistence, and structured report generation. Triggers on "deep research", "comprehensive analysis", "research report", "compare X vs Y",…

---
name: deep-research
description: Use when the user needs multi-source research with citation tracking, evidence persistence, and structured report generation. Triggers on "deep research", "comprehensive analysis", "research report", "compare X vs Y", "analyze trends", or "state of the art". Not for simple lookups, debugging, or questions answerable with 1-2 searches.
---

# Deep Research

## Core Purpose

Deliver citation-tracked research reports through a structured pipeline with evidence persistence, source identity management, claim-level verification, and progressive context management.

**Autonomy Principle:** Operate independently. Infer assumptions from context. Only stop for critical errors or incomprehensible queries. Surface high-materiality assumptions explicitly in the Introduction and Methodology rather than silently defaulting.

---

## Decision Tree

```
Request Analysis
+-- Simple lookup? --> STOP: Use WebSearch
+-- Debugging? --> STOP: Use standard tools
+-- Complex analysis needed? --> CONTINUE

Mode Selection
+-- Initial exploration --> quick (3 phases, 2-5 min)
+-- Standard research --> standard (6 phases, 5-10 min) [DEFAULT]
+-- Critical decision --> deep (8 phases, 10-20 min)
+-- Comprehensive review --> ultradeep (8+ phases, 20-45 min)
```

**Default assumptions:** Technical query = technical audience. Comparison = balanced perspective. Trend = recent 1-2 years.

---

## Workflow Overview

| Phase | Name | Quick | Std | Deep | Ultra |
|-------|------|-------|-----|------|-------|
| 1 | SCOPE | Y | Y | Y | Y |
| 2 | PLAN | - | Y | Y | Y |
| 3 | RETRIEVE | Y | Y | Y | Y |
| 4 | TRIANGULATE | - | Y | Y | Y |
| 4.5 | OUTLINE REFINEMENT | - | Y | Y | Y |
| 5 | SYNTHESIZE | - | Y | Y | Y |
| 6 | CRITIQUE | - | - | Y | Y |
| 7 | REFINE | - | - | Y | Y |
| 8 | PACKAGE | Y | Y | Y | Y |

**Note:** Phases 3-5 operate as an evidence loop per section (retrieve → evidence store → refine outline → draft → verify claims → delta-retrieve if needed), not as strict sequential gates.

---

## Execution

**On invocation, load relevant reference files:**

1. **Phase 1-7:** Load [methodology.md](./reference/methodology.md) for detailed phase instructions
2. **Phase 8 (Report):** Load [report-assembly.md](./reference/report-assembly.md) for progressive generation
3. **HTML/PDF output:** Load [html-generation.md](./reference/html-generation.md)
4. **Quality checks:** Load [quality-gates.md](./reference/quality-gates.md)
5. **Long reports (>18K words):** Load [continuation.md](./reference/continuation.md)

**Templates:**
- Report structure: [report_template.md](./templates/report_template.md)
- HTML styling: [mckinsey_report_template.html](./templates/mckinsey_report_template.html)

**Scripts:**
- `python scripts/validate_report.py --report [path]`
- `python scripts/verify_citations.py --report [path]`
- `python scripts/md_to_html.py [markdown_path]`

---

## Output Contract

**Required sections:**
- Executive Summary (200-400 words)
- Introduction (scope, methodology, assumptions)
- Main Analysis (4-8 findings, 600-2,000 words each, cited)
- Synthesis & Insights (patterns, implications)
- Limitations & Caveats
- Recommendations
- Bibliography (COMPLETE - every citation, no placeholders)
- Methodology Appendix

**Output files (all to `~/Documents/[Topic]_Research_[YYYYMMDD]/`):**
- Markdown (primary source of truth)
- `sources.jsonl` — stable source registry with canonical IDs
- `evidence.jsonl` — append-only evidence store with quotes and locators
- `claims.jsonl` — atomic claim ledger with support status
- `run_manifest.json` — query, mode, assumptions, provider config
- HTML (McKinsey style, auto-opened)
- PDF (professional print, auto-opened)

**Quality standards:**
- 10+ sources, 3+ per major claim (cluster-independent, not just count)
- All factual claims cited immediately [N] with evidence backing in `evidence.jsonl`
- Claim-support verification mandatory: no unsupported factual claims pass delivery
- No placeholders, no fabricated citations
- Prose-first (>=80%), bullets sparingly

---

## When to Use / NOT Use

**Use:** Comprehensive analysis, technology comparisons, state-of-the-art reviews, multi-perspective investigation, market analysis.

**Do NOT use:** Simple lookups, debugging, 1-2 search answers, quick time-sensitive queries.

Excerpt, first 4,324 characters of SKILL.md, verbatim from the audited commit. It is text from someone else’s repository, quoted so you can judge it before your agent reads it.

1. 2026-10-20
   ✓SAFE B 89 / 100

   first audit · source d875b0736241

Questions about deep-research

• github.com/199-biotechnologies/claude-deep-research-skill — the audited source at commit d875b0736241 and every finding aboveObserved · 20 Oct 2026

Spotted something wrong? Report a correction · Methodology