bio-longread-medaka

bio-longread-medaka is a skill for Claude Code, Codex from FreedomIntelligence/OpenClaw-Medical-Skills. It costs 52 tokens per session (1,420 once invoked), scanned A, original, no licence file.

A workflow for polishing genome assemblies and calling variants from Oxford Nanopore data with medaka, a neural-network-based tool.

In plain words
What is it for?
Use it to polish ONT assemblies or call variants directly from nanopore data.
Why use it?
It can improve assemblies made only from nanopore reads and identify variants without short-read polishing.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

Good fit Use it to polish ONT assemblies or call variants directly from nanopore data.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/freedomintelligence/openclaw-medical-skills/bio-longread-medaka
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-longread-medaka
Clone the repo
git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for bio-longread-medaka

README.md
[![agentmods](https://agentmods.dev/badge/skills/freedomintelligence/openclaw-medical-skills/bio-longread-medaka/github.svg)](https://agentmods.dev/skills/freedomintelligence/openclaw-medical-skills/bio-longread-medaka)
Your own site
<a href="https://agentmods.dev/skills/freedomintelligence/openclaw-medical-skills/bio-longread-medaka"><img src="https://agentmods.dev/badge/skills/freedomintelligence/openclaw-medical-skills/bio-longread-medaka/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for bio-longread-medaka

Your own site · 80×15
<a href="https://agentmods.dev/skills/freedomintelligence/openclaw-medical-skills/bio-longread-medaka"><img src="https://agentmods.dev/badge/skills/freedomintelligence/openclaw-medical-skills/bio-longread-medaka.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 52 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,420 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00052 $0.01420
Opus 5 $0.00026 $0.00710
Sonnet 5 $0.00010 $0.00284
Haiku 4.5 $0.00005 $0.00142

Measured 9d ago against content hash 3d3c9ad4249a, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

bio-longread-medaka scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.

The scan reads SKILL.md. This mod also ships 2 executable files (examples/medaka_polish.sh, examples/medaka_variant.sh), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/bio-longread-medaka/SKILL.md · 177 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

Read it on GitHub

Files

What ships with it

3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 9d ago First seen · 177 lines · 52 tokens per session scan A 3d3c9ad4249a

Subscribe to this mod's changes

bio-longread-medaka is a skill published in the GitHub repository FreedomIntelligence/OpenClaw-Medical-Skills (3,004 stars, last pushed 1mo ago), with no licence file. It adds 52 tokens to every session and 1,420 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

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