# Salmon Quantifier

> Salmon Quantifier is an Agent Skill for documents published in the a5c-ai/babysitter repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.

Salmon pseudo-alignment skill for fast and accurate transcript quantification

- Skill name: `salmon-quantifier`
- Category: [Documents](https://www.openparable.com/skill/documents/1)
- Source: https://github.com/a5c-ai/babysitter/blob/HEAD/library/specializations/domains/science/bioinformatics/skills/salmon-quantifier/SKILL.md
- Repository: a5c-ai/babysitter (1,548 GitHub stars when collected)

## SKILL.md

# 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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Source: https://www.openparable.com/skill/documents/salmon-quantifier (OpenParable). Cite the canonical URL above.