ClaudSkills / Science & Research / biology-medicine

bio-genome-assembly-scaffolding

Q: What is a Claude Code skill and how does the bio-genome-assembly-scaffolding 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-genome-assembly-scaffolding 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

type:generator

Orders and orients assembled contigs into chromosome-scale scaffolds from long-range linking data, inserting N-gap spacers (adds no sequence). Covers Hi-C/Omni-C scaffolding (YaHS, SALSA2, 3D-DNA/Juicer), Hi-C read-mapping prerequisites (map each end separately, no mate rescue, dedup, enzyme-aware), reading the contact map for misjoins/inversions/false-duplications, manual curation in Juicebox/PretextView (the VGP/DToL standard), reference-guided scaffolding (RagTag) and its karyotype-erasure hazard, genetic-map (ALLMAPS) and Bionano optical-map integration, chimera-breaking before scaffolding, gap-filling, and telomere/contig-vs-scaffold-N50 QC (tidk). Use when turning contigs into chromosomes with Hi-C, integrating a linkage map or optical map, choosing a scaffolder by available linking data, or judging whether a chromosome-scale assembly is trustworthy.

Security AStatic scan found no risk patternsHow grading works ›

What this skill does

bio-genome-assembly-scaffolding 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-genome-assembly-scaffolding--skills-scaffolding/ and loads when your prompt matches the skill's trigger.

When to invoke it: Use when turning contigs into chromosomes with Hi-C, integrating a linkage map or optical map, choosing a scaffolder by available linking data, or judging whether a chromosome-scale assembly is trustworthy.

Who uses this skill

The bio-genome-assembly-scaffolding 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 146,000+ 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-genome-assembly-scaffolding--skills-scaffolding
curl -L https://claudskills.com/skills/bio-genome-assembly-scaffolding--skills-scaffolding/SKILL.md \
  -o ~/.claude/skills/bio-genome-assembly-scaffolding--skills-scaffolding/SKILL.md

Or just download SKILL.md directly and drop it into ~/.claude/skills/bio-genome-assembly-scaffolding--skills-scaffolding/. Claude Code auto-discovers it on next session.

Skills live at ~/.claude/skills/bio-genome-assembly-scaffolding--skills-scaffolding/SKILL.md on macOS/Linux, or %USERPROFILE%\.claude\skills\bio-genome-assembly-scaffolding--skills-scaffolding\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-genome-assembly-scaffolding Claude Code skill?

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

What does the bio-genome-assembly-scaffolding 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-genome-assembly-scaffolding skill?

Use bio-genome-assembly-scaffolding 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-genome-assembly-scaffolding" 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-genome-assembly-scaffolding 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-genome-assembly-scaffolding 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-genome-assembly-scaffolding__skills-scaffolding/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-genome-assembly-scaffolding [Claude Code skill]. ClaudSkills. https://claudskills.com/skills/bio-genome-assembly-scaffolding--skills-scaffolding/

BibTeX

@misc{bio-genome-assembly-scaffolding--skills-scaffolding-2026,
  author    = {bg-szy},
  title     = {bio-genome-assembly-scaffolding [Claude Code skill]},
  year      = {2026},
  publisher = {ClaudSkills},
  url       = {https://claudskills.com/skills/bio-genome-assembly-scaffolding--skills-scaffolding/}
}

Embed this skill

Promote, attribute, or link this skill from your own README, blog post, or documentation. All three snippets are free to use — no sign-up, no API key. More distribution surfaces →

Badge

[![ClaudSkills](https://claudskills.com/badge/bio-genome-assembly-scaffolding--skills-scaffolding.svg)](https://claudskills.com/skills/bio-genome-assembly-scaffolding--skills-scaffolding/?utm_source=badge&utm_medium=readme&utm_campaign=skill_badge)

Security scan

Grade A · scanned 2026-07-06 — 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

Show this grade on your repo (click to copy):

[![Security: A](https://img.shields.io/badge/Security-A-2e7d32)](https://claudskills.com/skills/bio-genome-assembly-scaffolding--skills-scaffolding/#security)

More Science & Research skills

Browse all Science & Research skills in the ClaudSkills registry, or explore these other picks from the same category:

Browse all Science & Research skills → Top 100 skills

Part of ClaudSkills — the open registry for Claude Skills & Claude Code Skills. · What's New · Install guide · About · llms.txt

Part of Acreator Store — Adam Lankamer's AI tools: PerfectStudio · Ucaption · UTagger · AutoXPoster · TestYourSkills · AutomationFlows · Au Naturel · Telegram @acreatorstore