Deep Research Workflow
TokenRhythm/opensquilla
Runs multi-round research in three stages with a persisted state file, evidence tracking and a long-form report with per-claim citations.
A skill your agent uses when a decision-relevant question needs multi-source search, claim-level citations, contradiction handling, uncertainty, or a durable wiki handoff.
Install Deep Research
$ npx skills add Mark393295827/third-brain-v7-skills --skill deep-research -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install Mark393295827/third-brain-v7-skills deep-research --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/Mark393295827/third-brain-v7-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/deep-research .claude/skills/deep-research && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "deep-research" agent skill from https://github.com/Mark393295827/third-brain-v7-skills/tree/main/skills/deep-research into .claude/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/Mark393295827/third-brain-v7-skills/tree/main/skills/deep-researchType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add Mark393295827/third-brain-v7-skills --skill deep-research -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install Mark393295827/third-brain-v7-skills deep-research --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Mark393295827/third-brain-v7-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/deep-research .agents/skills/deep-research && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "deep-research" agent skill from https://github.com/Mark393295827/third-brain-v7-skills/tree/main/skills/deep-research into .agents/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add Mark393295827/third-brain-v7-skills --skill deep-research -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install Mark393295827/third-brain-v7-skills deep-research --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Mark393295827/third-brain-v7-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/deep-research .cursor/skills/deep-research && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "deep-research" agent skill from https://github.com/Mark393295827/third-brain-v7-skills/tree/main/skills/deep-research into .cursor/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/Mark393295827/third-brain-v7-skills.git --path skills/deep-research--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add Mark393295827/third-brain-v7-skills --skill deep-research -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install Mark393295827/third-brain-v7-skills deep-research --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Mark393295827/third-brain-v7-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/deep-research .gemini/skills/deep-research && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "deep-research" agent skill from https://github.com/Mark393295827/third-brain-v7-skills/tree/main/skills/deep-research into .gemini/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install Mark393295827/third-brain-v7-skills deep-researchInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add Mark393295827/third-brain-v7-skills --skill deep-research -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/Mark393295827/third-brain-v7-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/deep-research .github/skills/deep-research && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "deep-research" agent skill from https://github.com/Mark393295827/third-brain-v7-skills/tree/main/skills/deep-research into .github/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add Mark393295827/third-brain-v7-skills --skill deep-research -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install Mark393295827/third-brain-v7-skills deep-research --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Mark393295827/third-brain-v7-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/deep-research .opencode/skills/deep-research && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "deep-research" agent skill from https://github.com/Mark393295827/third-brain-v7-skills/tree/main/skills/deep-research into .opencode/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
deep-research- GitHub stars
- 141
- Token cost
- ~1.5k tokens
- SKILL.md length
- 636 words
- Files
- 2 (incl. references)
- Skills in repo
- 21
- Repo updated
- First seen
- Licence
- MIT
At a glance
A skill your agent uses when a decision-relevant question needs multi-source search, claim-level citations, contradiction handling, uncertainty, or a durable wiki handoff.
- Works in 9 steps: Run a broad discovery pass; rank sources… → Prefer primary and official evidence for… → Build a source ledger and claim ledger… → …
- A decision-relevant question needs multi-source search
- SKILL.md covers Usage Template, Workflow, Failure Protocol and Output Contract, plus 3 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Deep Research is an agent skill from Mark393295827/third-brain-v7-skills. Use when a decision-relevant question needs multi-source search, claim-level citations, contradiction handling, uncertainty, or a durable wiki handoff.
Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files, including reference files (for example `references/research-ledgers.md`).
It sits in Research & Science, covering Deep research and Citation management. The repository describes itself as: agent wiki +engineering skills. The licence is MIT.
When your agent uses it
- A decision-relevant question needs multi-source search
- Claim-level citations
- Contradiction handling
- A durable wiki handoff
Example prompts
- “/deep-research”
Workflow steps
9 steps, taken from the first numbered list in SKILL.md.
- Run a broad discovery pass; rank sources by authority, directness, recency, independence, and relevance.
- Prefer primary and official evidence for consequential claims; use secondary sources for context and disagreement discovery.
- Build a source ledger and claim ledger while reading, not after drafting.
- Triangulate central claims; record dates and whether sources are independent or repeating one origin.
- Run a gap-fill pass only for decision-critical unknowns.
- Draft an answer-first synthesis separating evidence, inference, uncertainty, disagreement, and implications.
- Run an adversarial pass: strongest counterevidence, alternative mechanism, stale data, selection bias, and missing base rate.
- For science/AI experiments, specify problem, data/simulator, intervention, objective metric, uncertainty, reproducibility, and human…
- Produce an activity trace and, when requested, a STOW handoff packet for wiki-ingest rather than writing source claims directly into…
What it can do on your machine
Read from SKILL.md and the folder at commit 5a64514. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Deep Research loads about 1.5k tokens when it runs, and up to ~1.9k if it reads all its reference files. Until then it costs about 41 tokens; SKILL.md has 636 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from Mark393295827/third-brain-v7-skills at commit 5a64514, republished under its MIT licence (© Mark393295827). 636 words, ~1,465 tokens.
Download SKILL.mdSave it as
.claude/skills/deep-research/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.- name
- deep-research
- description
- Use when a decision-relevant question needs multi-source search, claim-level citations, contradiction handling, uncertainty, or a durable wiki handoff.
- metadata.version
- 8.1.0
- metadata.updated
- 2026-08-18
- metadata.profile
- high-risk
- metadata.assumes
- The question benefits from multiple sources and authorized source access is available.
- metadata.conflicts_with
- Link collection without synthesis, uncited material claims, privacy leakage, or autonomous experiments without objective evaluation.
Deep Research
<skill_contract>
<input>Decision-relevant question, audience, scope, recency, source and privacy boundaries, budget, and required deliverable.</input>
<output>An answer-first synthesis with source and claim ledgers, citations, contradictions, uncertainty, and durable handoff.</output>
<done>Decision-critical claims are traceable and adversarially checked, unresolved gaps are explicit, and the stop rule is met.</done>
<non_goals>Link collection, uncited material claims, privacy leakage, exhaustive search, or autonomous high-impact experiments.</non_goals>
Research is an evidence loop, not a volume contest. Define the decision, gather the minimum diverse evidence, maintain source and claim ledgers, attack the synthesis, then stop when additional search no longer changes the answer.
Usage Template
Provide: research question, audience/decision, scope, recency, allowed/excluded sources, privacy boundary, budget, output format, and wiki destination if durable. Load references/research-ledgers.md for ledger schemas.
Workflow
<intake>Choose one mode: evidence brief, knowledge curation, recency pulse, domain intelligence, scientific-method audit, or heavy research. Convert the question into 3-7 information requirements, decision criteria, interruption points, and a source-access plan.
</intake><unknowns_gate>
If the decision, recency window, private-data authority, or source boundary materially changes the result, return NEEDS_INPUT. Record known, probeable, testable, and inaccessible unknowns. Do not treat inaccessible sources as supporting evidence.
</unknowns_gate>
<execute>- Run a broad discovery pass; rank sources by authority, directness, recency, independence, and relevance.
- Prefer primary and official evidence for consequential claims; use secondary sources for context and disagreement discovery.
- Build a source ledger and claim ledger while reading, not after drafting.
- Triangulate central claims; record dates and whether sources are independent or repeating one origin.
- Run a gap-fill pass only for decision-critical unknowns.
- Draft an answer-first synthesis separating evidence, inference, uncertainty, disagreement, and implications.
- Run an adversarial pass: strongest counterevidence, alternative mechanism, stale data, selection bias, and missing base rate.
- For science/AI experiments, specify problem, data/simulator, intervention, objective metric, uncertainty, reproducibility, and human judgment boundary.
- Produce an activity trace and, when requested, a STOW handoff packet for
wiki-ingestrather than writing source claims directly into governed concepts.
For high-stakes conclusions, use independent review. Obtain approval before accessing private systems, publishing, or launching experiments. Any durable write needs a diff-based rollback path.
</execute><evaluate>Audit every material claim against the ledger. Check citation entailment, source independence, freshness, contradiction coverage, privacy, and whether the recommendation changes under plausible uncertainty. Stop when new searches repeat known evidence or cannot change the decision.
</evaluate><retry_policy>
max_attempts: 3 research passes: discovery, gap-fill, adversarial. A retry must target a named gap with a changed query/source class. Stop on duplicate evidence, repeated access failure, or NO_PROGRESS.
</retry_policy>
<state_contract>
Persist {run_id, status, attempt, budget, evidence, unknowns, last_error, next_action} plus question version, mode, information requirements, source/claim ledgers, search trace, contradictions, privacy decisions, approval, draft version, and rollback/write receipts.
</state_contract>
Show full SKILL.md (188 more words)Show less
Failure Protocol
NEEDS_INPUT: scope, decision, privacy, or freshness boundary is ambiguous.INSUFFICIENT_EVIDENCE: sources cannot support the requested confidence or recommendation.BLOCKED_PERMISSION: private or restricted evidence is unavailable; exclude it explicitly.VERIFY_FAILED: citation does not entail the claim or key contradiction is unresolved.NO_PROGRESS: a changed pass yields no decision-relevant evidence.BUDGET_STOP: synthesize covered scope and list gaps.max_attempts: 3.
Output Contract
Return status, result (answer-first synthesis and recommendation), evidence (claim/source ledgers and citations), unknowns, and next_action including approval or wiki handoff.
Edge Cases
- Ten articles repeat one press release: count one underlying evidence origin and lower independence confidence.
- Sources disagree on a current metric: show dated values and definitions, explain the mismatch, and withhold a false single number.
Success Metrics
- Material claims have direct, current, claim-level support.
- Disagreements and confidence are visible where they affect the decision.
- Search stops by evidence saturation or budget, not arbitrary link count.
Quality Gates
- Decision, scope, recency, privacy, and source boundaries are explicit.
- Source and claim ledgers are inspectable.
- Independent/adversarial verification covers central claims.
- Approval and rollback controls cover external actions and durable writes.
- Handoff preserves source provenance and unresolved gaps.
</skill_contract>
© Mark393295827, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 1 other file (references) in skills/deep-research of Mark393295827/third-brain-v7-skills.
- SKILL.md
- references/research-ledgers.md
Open the folder on GitHubat commit 5a64514
Compare with similar skills
Deep Research next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Deep Research this skillMark393295827/third-brain-v7-skills | 141 | — | ~1.5k | Automated safety check: Pass | MIT | |
| Deep Research WorkflowTokenRhythm/opensquilla | 7.1k | — | ~1.3k | Automated safety check: Pass | Apache-2.0 | |
| Academic Research Suite for CodexImbad0202/academic-research-skills-codex | 12k | — | ~12k | Automated safety check: Pass | Custom licence | |
| Deep Research Literature SurveyHKUSTDial/Supervisor-Skills | 8.7k | — | ~2.4k | Automated safety check: Pass | CC-BY-NC-SA-4.0 | |
| Parallel WebLeonChaoX/qinyan-academic-skills | 943 | 1 repos | ~2.9k | Automated safety check: Notes | MIT | |
| Live Researchbrightdata/skills | 264 | — | ~1.8k | Automated safety check: Pass | MIT |
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Academic Research Suite for Codex
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Deep Research Literature Survey
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Runs a survey-grade literature investigation: fixes the research questions, searches from adversarial angles, verifies citations and writes an evidence-first report.
Parallel Web
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Live Research
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Deep Research Methodology
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Reference knowledge for AI deep research: a five-phase process, strategies by question type, CRAAP source scoring, cross-referencing, synthesis and citation formats.
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Related
Categories
Questions about Deep Research
What does Deep Research do?
A skill your agent uses when a decision-relevant question needs multi-source search, claim-level citations, contradiction handling, uncertainty, or a durable wiki handoff. Deep Research is an agent skill from Mark393295827/third-brain-v7-skills. Use when a decision-relevant question needs multi-source search, claim-level citations, contradiction handling, uncertainty, or a durable wiki handoff.
When should I use Deep Research?
Deep Research fits situations like: A decision-relevant question needs multi-source search; claim-level citations; contradiction handling; A durable wiki handoff.
How do I install Deep Research in Claude Code?
Run `npx skills add Mark393295827/third-brain-v7-skills --skill deep-research -a claude-code`. Or copy the skill folder (skills/deep-research in Mark393295827/third-brain-v7-skills) into .claude/skills/deep-research in your project. Claude Code loads it when a task matches its description.
How do I install Deep Research in Codex?
Run `npx skills add Mark393295827/third-brain-v7-skills --skill deep-research -a codex`. Or copy the skill folder (skills/deep-research in Mark393295827/third-brain-v7-skills) into .agents/skills/deep-research in your project. Codex loads it when a task matches its description.
Can I use Deep Research in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add Mark393295827/third-brain-v7-skills --skill deep-research -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/deep-research, .gemini/skills/deep-research, .github/skills/deep-research and .opencode/skills/deep-research in your project.
What does Deep Research need to run?
SKILL.md names no scripts, command-line tools or credentials: Deep Research is instructions for the agent only.
Does Deep Research access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Deep Research safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Deep Research use?
Deep Research is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Deep Research use?
About 1.5k tokens (SKILL.md is roughly 5.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 420 tokens, read only when the agent opens those files.
What are the alternatives to Deep Research?
Skills that share tags, products or a category with Deep Research: Deep Research Workflow (TokenRhythm/opensquilla, 7.1k stars), Academic Research Suite for Codex (Imbad0202/academic-research-skills-codex, 12k stars), Deep Research Literature Survey (HKUSTDial/Supervisor-Skills, 8.7k stars) and Parallel Web (LeonChaoX/qinyan-academic-skills, 943 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Deep Research?
Mark393295827 (a GitHub user) maintains it in Mark393295827/third-brain-v7-skills, which has 141 GitHub stars. The repository holds 21 skills in this directory. The repository was last updated on September 19, 2026.
Source: Mark393295827/third-brain-v7-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.