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Agent skill

Bio Longread Structural Variants

by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills

Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM.

No licenceAuto-check passed

Install Bio Longread Structural Variants

skills CLI
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-longread-structural-variants -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-longread-structural-variants --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-longread-structural-variants .claude/skills/bio-longread-structural-variants && rm -rf skills-src

Use ~/.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/

Facts

Skill name
bio-longread-structural-variants
GitHub stars
3.1k
Used in
1 other repo
Token cost
~1.4k tokens
SKILL.md length
287 words
Files
3
Skills in repo
170
Repo updated
First seen
Licence
None found

At a glance

Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM.

  • Detecting deletions
  • SKILL.md covers Version Compatibility, Sniffles2 - Basic SV Calling, Sniffles2 - Common Options and Sniffles2 - Population Calling, plus 13 more sections
  • Runs Shell scripts from its folder
  • Complex rearrangements from ONT

What it does

Bio Longread Structural Variants is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, insertions, inversions, translocations, or complex rearrangements from ONT or PacBio data, especially those missed by short-read methods.

Its SKILL.md is about 1.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/sv_calling.sh` and `usage-guide.md`).

The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.

When your agent uses it

  • Detecting deletions
  • Complex rearrangements from ONT
  • Especially those missed by short-read methods

Example prompts

  • “/bio-longread-structural-variants”

Requirements

  • A Bash shell

What it can do on your machine

Read from SKILL.md and the folder at commit b1f9b6e. 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

    Ships script files (Shell), which the agent can run.

    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

Bio Longread Structural Variants loads about 1.4k tokens when it runs. Until then it costs about 72 tokens; SKILL.md has 287 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~72
When it runs · the whole SKILL.md, loaded when a task matches
~1.4k

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

Without a licence we can't republish the file, so here is its outline and opening line. It has 287 words (~1,424 tokens).

“Reference examples tested with: bcftools 1.19+”

— opening of SKILL.md by FreedomIntelligence
name
bio-longread-structural-variants
tool_type
cli
primary_tool
sniffles

Read the full SKILL.md on GitHub

Files

SKILL.md and 2 other files in skills/bio-longread-structural-variants of FreedomIntelligence/OpenClaw-Medical-Skills.

  • SKILL.md
  • examples/sv_calling.sh
  • usage-guide.md

Open the folder on GitHubat commit b1f9b6e

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Bio Longread Structural Variants 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.

Bio Longread Structural Variants compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bio Longread Structural Variants this skillFreedomIntelligence/OpenClaw-Medical-Skills3.1k1 repos~1.4kAutomated safety check: PassNone
Bio Alignment StructuralGPTomics/bioSkills1.2k2 repos~5.9kAutomated safety check: PassMIT
Bio Variant Calling Structural Variant CallingGPTomics/bioSkills1.2k1 repos~7.2kAutomated safety check: PassMIT
Bio Long Read Sequencing Structural VariantsGPTomics/bioSkills1.2k1 repos~3.4kAutomated safety check: PassMIT
Bio Structural Biology Binding Site DetectionGPTomics/bioSkills1.2k1 repos~4.8kAutomated safety check: PassMIT
Bio Structural Biology Structure IoGPTomics/bioSkills1.2k1 repos~4kAutomated safety check: PassMIT

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  • Bio Alignment Structural

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  • Bio Variant Calling Structural Variant Calling

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  • Bio Long Read Sequencing Structural Variants

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  • Bio Structural Biology Binding Site Detection

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Questions about Bio Longread Structural Variants

What does Bio Longread Structural Variants do?

Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Bio Longread Structural Variants is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM.

When should I use Bio Longread Structural Variants?

Bio Longread Structural Variants fits situations like: detecting deletions; complex rearrangements from ONT; especially those missed by short-read methods.

How do I install Bio Longread Structural Variants in Claude Code?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-longread-structural-variants -a claude-code`. Or copy the skill folder (skills/bio-longread-structural-variants in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-longread-structural-variants in your project. Claude Code loads it when a task matches its description.

How do I install Bio Longread Structural Variants in Codex?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-longread-structural-variants -a codex`. Or copy the skill folder (skills/bio-longread-structural-variants in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-longread-structural-variants in your project. Codex loads it when a task matches its description.

Can I use Bio Longread Structural Variants 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-longread-structural-variants -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-longread-structural-variants, .gemini/skills/bio-longread-structural-variants, .github/skills/bio-longread-structural-variants and .opencode/skills/bio-longread-structural-variants in your project.

What does Bio Longread Structural Variants need to run?

Going by SKILL.md and its folder, Bio Longread Structural Variants needs a shell for the scripts in its folder. Our summary lists: A Bash shell.

Does Bio Longread Structural Variants 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 Bio Longread Structural Variants 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 Bio Longread Structural Variants use?

No licence was found for Bio Longread Structural Variants or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.

How many tokens does Bio Longread Structural Variants use?

About 1.4k tokens (SKILL.md is roughly 5.7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Bio Longread Structural Variants?

Skills that share tags, products or a category with Bio Longread Structural Variants: Bio Alignment Structural (GPTomics/bioSkills, 1.2k stars), Bio Variant Calling Structural Variant Calling (GPTomics/bioSkills, 1.2k stars), Bio Long Read Sequencing Structural Variants (GPTomics/bioSkills, 1.2k stars) and Bio Structural Biology Binding Site Detection (GPTomics/bioSkills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bio Longread Structural Variants?

FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,052 GitHub stars. The repository holds 170 skills in this directory. The repository was last updated on July 21, 2026.

Source: FreedomIntelligence/OpenClaw-Medical-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.