# Salmon Quantifier

> Salmon pseudo-alignment skill for fast and accurate transcript quantification

- Skill: `a5c-ai/salmon-quantifier` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/salmon-quantifier`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/salmon-quantifier/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/salmon-quantifier

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# 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)