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Salmon quantifier

Skill a5c-ai/babysitter/library/specializations/domains/science/bioinformatics/skills/salmon-quantifier

Salmon pseudo-alignment skill for fast and accurate transcript quantificationFrom its SKILL.md

Install
npx -y skills add a5c-ai/babysitter --skill salmon-quantifier

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.4 KB, 159 tokens by cl100k_base, as published. Nobody here has run it

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)

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.

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