bio-rna-quantification-alignment-free-quant

bio-rna-quantification-alignment-free-quant is a skill for Claude Code, Codex from FridrichMethod/awesome-skills. It costs 95 tokens per session (2,741 once invoked), scanned A, original, no licence file.

A method for measuring transcript activity from FASTQ files, which contain raw RNA-sequencing reads, without first mapping those reads to a genome. It uses Salmon or kallisto and can check library strand direction and apply listed bias corrections.

In plain words
What is it for?
It helps quantify RNA-seq expression, choose or check the needed index, verify library strandedness, and apply GC or sequence-bias correction.
Why use it?
It avoids a separate genome-mapping step when the goal is to estimate how much RNA each transcript produced.

Skill for Claude CodeCodex

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.

agentmods
npx agentmods add skills/fridrichmethod/awesome-skills/alignment-free-quant
Any agent
npx skills add FridrichMethod/awesome-skills --skill alignment-free-quant
Clone the repo
git clone --depth 1 https://github.com/FridrichMethod/awesome-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-rna-quantification-alignment-free-quant

README.md
[![agentmods](https://agentmods.dev/badge/skills/fridrichmethod/awesome-skills/alignment-free-quant.svg)](https://agentmods.dev/skills/fridrichmethod/awesome-skills/alignment-free-quant)
Your own site
<a href="https://agentmods.dev/skills/fridrichmethod/awesome-skills/alignment-free-quant"><img src="https://agentmods.dev/badge/skills/fridrichmethod/awesome-skills/alignment-free-quant.svg" alt="Measured on agentmods" height="20"></a>
Per session 95 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,741 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
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 $0.00095 $0.02741
Opus 5 $0.00048 $0.01371
Sonnet 5 $0.00019 $0.00548
Haiku 4.5 $0.00010 $0.00274

Measured 5d ago against content hash d8a61bb9dc40, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

bio-rna-quantification-alignment-free-quant 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 5d ago.

The scan reads SKILL.md. This mod also ships 2 executable files (examples/kallisto_quant.sh, examples/salmon_quant.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/alignment-free-quant/SKILL.md · 154 lines

The source is not reproduced here

A licence we could not identify

The repository carries a LICENSE file, but it is custom or dual enough that GitHub cannot name it and neither can this catalogue. Unknown terms are not permission, so the body is not copied here. Read the licence at the source and decide for yourself.

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. 5d ago First seen · 154 lines · 95 tokens per session scan A d8a61bb9dc40

Subscribe to this mod's changes

bio-rna-quantification-alignment-free-quant is a skill published in the GitHub repository FridrichMethod/awesome-skills (14 stars, last pushed 6d ago), with no licence file. It adds 95 tokens to every session and 2,741 once invoked, about $0.0005 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 2026-08-30.

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