salmon-quantifier

Salmon pseudo-alignment skill for fast and accurate transcript quantification

509 stars

bya5c-ai

View on GitHub Installation ↓

Best use case

salmon-quantifier is best used when you need a repeatable AI agent workflow instead of a one-off prompt.

Salmon pseudo-alignment skill for fast and accurate transcript quantification

Teams using salmon-quantifier should expect a more consistent output, faster repeated execution, less prompt rewriting.

When to use this skill

You want a reusable workflow that can be run more than once with consistent structure.

When not to use this skill

You only need a quick one-off answer and do not need a reusable workflow.
You cannot install or maintain the underlying files, dependencies, or repository context.

Installation

Claude Code / Cursor / Codex

$curl -o ~/.claude/skills/salmon-quantifier/SKILL.md --create-dirs "https://raw.githubusercontent.com/a5c-ai/babysitter/main/library/specializations/domains/science/bioinformatics/skills/salmon-quantifier/SKILL.md"

Manual Installation

Download SKILL.md from GitHub
Place it in .claude/skills/salmon-quantifier/SKILL.md inside your project
Restart your AI agent — it will auto-discover the skill

How salmon-quantifier Compares

Feature / Agent	salmon-quantifier	Standard Approach
Platform Support	Not specified	Limited / Varies
Context Awareness	High	Baseline
Installation Complexity	Unknown	N/A

Frequently Asked Questions

What does this skill do?

Salmon pseudo-alignment skill for fast and accurate transcript quantification

Where can I find the source code?

You can find the source code on GitHub using the link provided at the top of the page.

SKILL.md Source

# Salmon Quantifier Skill

## Purpose
Enable Salmon pseudo-alignment for fast and accurate transcript quantification.

## Capabilities
- Selective alignment mode
- GC bias correction
- Mapping rate assessment
- Bootstrap uncertainty estimation
- Multi-mapping resolution
- Decoy-aware indexing

## Usage Guidelines
- Build decoy-aware indices for accuracy
- Enable GC bias correction
- Use selective alignment for improved accuracy
- Generate bootstraps for uncertainty estimation
- Validate mapping rates against expectations
- Document index and parameter versions

## Dependencies
- Salmon
- kallisto
- RSEM

## Process Integration
- RNA-seq Differential Expression Analysis (rnaseq-differential-expression)
- Single-Cell RNA-seq Analysis (scrnaseq-analysis)

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