Deep Research

Install

git clone https://github.com/199-biotechnologies/claude-deep-research-skill.git ~/.claude/skills/deep-research

This is third-party code. Review the repository files before installing.

What it does

The skill runs research through a multi-phase pipeline: scoping, planning, parallel retrieval with sub-agents, triangulation, outline refinement, synthesis, critique, refinement and packaging. Four depth modes range from a quick scan to an exhaustive report. Sources and citations are persisted to disk, so they survive context compaction, and long reports continue via new agents. Bundled Python scripts validate report structure, score source credibility and detect fabricated links and DOIs.

Who it is for. For analysts, researchers and managers who need a thorough report with verifiable sources.

Example request

deep research in deep mode: compare PostgreSQL vs Supabase for our stack

Limitations

Deep modes take tens of minutes and use many tokens. For better search the author recommends search-cli with Brave, Serper, Exa, Jina or Firecrawl keys; otherwise built-in WebSearch is used. PDF output needs WeasyPrint. The README states MIT, but GitHub detects no license file.

How to disable. Delete the ~/.claude/skills/deep-research folder.

Security check

• Makes many web requests and runs Python scripts
• Writes report files to the home directory

README in short

The README covers installing by cloning into the skills directory and optional search-cli setup. It describes depth modes with durations, pipeline phases, output formats and quality standards: source counts, section length and automated report and citation checks. It also shows the skill layout and version history.

SKILL.md

---
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 |

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