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.
About this skill (catalog notes)
bio-genome-assembly-scaffolding includes pricing or quota commentary; at least one code block. At roughly 3,092 words the SKILL.md is on the longer end of the catalog distribution.
How bio-genome-assembly-scaffolding fits the catalog
bio-genome-assembly-scaffolding sits in the Science & Research category under the biology-medicine sub-topic in the ClaudSkills catalog. There are 10 related skills indexed alongside it; comparing a few before installing usually reveals which fits your workflow best.
These notes are auto-generated from features detected in the SKILL.md file and from this catalog's structure — they aren't part of the source repository.
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 93,000+ SKILL.md files for Anthropic's Claude Code agent and the wider Claude ecosystem (Claude API, Claude Agent SDK).
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.
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One-click install via the desktop app
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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?
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.
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/.
@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/}
}
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