Salmon Quantifier Skill
SkillDev toolsSalmon pseudo-alignment skill for fast and accurate transcript quantification
Instructions available. Your AI can read the instructions. Execution depends on the setup they require.
Account requirements not reviewed. Check the skill instructions before use; ahel provides instructions and does not run this skill.
Add ahel to your AI once: Claude, ChatGPT, Cursor, Claude Code or Codex. Then ask it to use this.
Then ask your AI: use the Salmon Quantifier Skill skill
What this skill tells your AI
The instructions your AI receives, as published by a5c-ai/babysitter in library/specializations/domains/science/bioinformatics/skills/salmon-quantifier/SKILL.md and read by ahel’s review.
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)
Signals
- GitHub stars
- 2k
- Forks
- 112
- Last commit
- Sep 2026
Advanced
- Item type
- skill
- Key
salmon-quantifier- Source
- github.com/a5c-ai/babysitter