ClaudSkills / Science & Research / biology-medicine

bio-epidemiological-genomics-transmission-inference

Q: How do I install the bio-epidemiological-genomics-transmission-inference Claude Code skill?

Install via the ClaudSkills desktop app (one click) or copy SKILL.md from the source repository to ~/.claude/skills/bio-epidemiological-genomics-transmission-inference--skills-tran/SKILL.md and restart Claude Code. Both flows are detailed at https://claudskills.com/install/.

Q: Is this skill free to install?

Yes. ClaudSkills is an open registry — every skill keeps its source repository's license, and manual install via copy is free. ClaudSkills Pro ($9/mo, $79/yr, or $149 one-time) adds one-click install via the desktop app and a multi-signal Quality Score.

Q: When should I use the bio-epidemiological-genomics-transmission-inference skill?

Use bio-epidemiological-genomics-transmission-inference when your Claude Code task falls under the Science & Research category — specifically in the biology medicine area. Claude Code auto-discovers installed skills and invokes the right one based on the task description, so you can also ask Claude directly (e.g. 'use bio-epidemiological-genomics-transmission-inference' or describe the task and let Claude pick). Browse related skills at https://claudskills.com/category/science/.

Q: What is a Claude Code skill and how does the bio-epidemiological-genomics-transmission-inference skill fit in?

A Claude Code skill is a SKILL.md file that lives under ~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. bio-epidemiological-genomics-transmission-inference is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Science & Research category. Learn more at https://claudskills.com/learn/what-is-skill-md/.

Category: Science & Research · Sub-category: biology-medicine · Last updated: 2026-06-02

Infers person-to-person transmission from pathogen genomes using outbreaker2 (Campbell 2018), TransPhylo (Didelot 2017), phybreak (Klinkenberg 2017), BadTrIP (De Maio 2018), SCOTTI (De Maio 2016), BEASTLIER (Hall 2015), and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines outbreak clusters using pathogen-specific SNP thresholds (NOT a universal cutoff -- TB <=12 SNPs / Walker 2013; MRSA <=15 / Coll 2017; C. difficile <=2 / Eyre 2013; Klebsiella <=21 / Snitkin 2012), models within-host diversity and transmission bottlenecks (Worby-Lipsitch-Hanage 2014; McCrone 2018; Sobel Leonard 2017; Lythgoe 2021 SARS-CoV-2), integrates contact-tracing data, distinguishes generation interval from serial interval (Britton & Scalia Tomba 2019; Ali 2020), attributes source via Bayesian source attribution (Mather 2013 DT104; islandR), and reconciles transmission-network reconstruction with epi metadata.

Security AStatic scan found no risk patternsHow grading works ›

What this skill does

bio-epidemiological-genomics-transmission-inference is a community-contributed Claude Code skill in the biology-medicine sub-category. It ships as a SKILL.md file that Claude Code auto-discovers under ~/.claude/skills/bio-epidemiological-genomics-transmission-inference--skills-tran/ and loads when your prompt matches the skill's trigger.

Who uses this skill

The bio-epidemiological-genomics-transmission-inference Claude Code skill is built for researchers, data scientists, academics, and analysts working with complex data and scientific literature. It's part of ClaudSkills (also referred to as Claude Skills or Claude Code Skills) — the open community-curated registry of 161,000+ SKILL.md files for Anthropic's Claude Code agent and the wider Claude ecosystem (Claude API, Claude Agent SDK).

How to install

Free

Manual install (2 steps)

mkdir -p ~/.claude/skills/bio-epidemiological-genomics-transmission-inference--skills-tran
curl -L https://claudskills.com/skills/bio-epidemiological-genomics-transmission-inference--skills-tran/SKILL.md \
  -o ~/.claude/skills/bio-epidemiological-genomics-transmission-inference--skills-tran/SKILL.md

Or just download SKILL.md directly and drop it into ~/.claude/skills/bio-epidemiological-genomics-transmission-inference--skills-tran/. Claude Code auto-discovers it on next session.

Skills live at ~/.claude/skills/bio-epidemiological-genomics-transmission-inference--skills-tran/SKILL.md on macOS/Linux, or %USERPROFILE%\.claude\skills\bio-epidemiological-genomics-transmission-inference--skills-tran\SKILL.md on Windows. See the full install guide for step-by-step instructions.

📱 Install from your phone or desktop Telegram

Open @claudskills_bot on Telegram, tap Open Desktop App, and the desktop app installs this skill for you. Or share the bot link with a colleague — they get the same one-tap install. Learn more →

Pro

One-click install via the desktop app

The ClaudSkills desktop app installs any skill directly into ~/.claude/skills/ with one click — no terminal required. Pro starts at $9/mo or $149 lifetime.

Pro

For the full experience including quality scoring and one-click install features for each skill — upgrade to Pro.

See pricing → Download desktop app

Frequently asked questions

How do I install the bio-epidemiological-genomics-transmission-inference Claude Code skill?

Install via the ClaudSkills desktop app (one click) or copy SKILL.md from the source repository to ~/.claude/skills/bio-epidemiological-genomics-transmission-inference--skills-tran/SKILL.md and restart Claude Code. Both flows are detailed at claudskills.com/install/.

What does the bio-epidemiological-genomics-transmission-inference skill do?

Is this skill free to install?

Yes. ClaudSkills is an open registry — every skill keeps its source repository's license, and manual install via copy is free. ClaudSkills Pro ($9/mo, $79/yr, or $149 one-time) adds one-click install via the desktop app and a multi-signal Quality Score.

When should I use the bio-epidemiological-genomics-transmission-inference skill?

Use bio-epidemiological-genomics-transmission-inference when your Claude Code task falls under the Science & Research category — specifically in the biology medicine area. Claude Code auto-discovers installed skills and invokes the right one based on the task description, so you can also ask Claude directly (e.g. "use bio-epidemiological-genomics-transmission-inference" or describe the task and let Claude pick). Browse related skills at /category/science/.

What is a Claude Code skill and how does the bio-epidemiological-genomics-transmission-inference skill fit in?

A Claude Code skill is a SKILL.md file that lives under ~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. bio-epidemiological-genomics-transmission-inference is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Science & Research category. Learn more at /learn/what-is-a-claude-skill/.

Attribution & license

Source: https://github.com/bg-szy/TOP-SKILLS/blob/HEAD/skills/awesome-skills/bio-epidemiological-genomics-transmission-inference__skills-transmission-inference/SKILL.md
Author: bg-szy
Website: https://bg-szy.github.io/TOP-SKILLS/

Cite this skill

If you reference this skill in a blog post, paper, or documentation, you can cite it as:

APA

bg-szy. (2026). bio-epidemiological-genomics-transmission-inference [Claude Code skill]. ClaudSkills. https://claudskills.com/skills/bio-epidemiological-genomics-transmission-inference--skills-tran/

BibTeX

@misc{bio-epidemiological-genomics-transmission-inference--skills-tran-2026,
  author    = {bg-szy},
  title     = {bio-epidemiological-genomics-transmission-inference [Claude Code skill]},
  year      = {2026},
  publisher = {ClaudSkills},
  url       = {https://claudskills.com/skills/bio-epidemiological-genomics-transmission-inference--skills-tran/}
}

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Badge

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Security scan

Grade A · scanned 2026-07-26 — free static scan against the OWASP Agentic Skills Top 10.

No risk patterns were found in any of the ten OWASP-aligned categories. How grading works ›

✓ Prompt injection
✓ Data exfiltration
✓ Supply chain
✓ Reverse shell
✓ Credentials
✓ Execution
✓ Filesystem
✓ Persistence
✓ Obfuscation
✓ Network

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[![Security: A](https://img.shields.io/badge/Security-A-2e7d32)](https://claudskills.com/skills/bio-epidemiological-genomics-transmission-inference--skills-tran/#security)

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