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claude-codescience

Babysitter salmon-quantifier

Salmon pseudo-alignment skill for fast and accurate transcript quantification

install
source · Clone the upstream repo
git clone https://github.com/a5c-ai/babysitter
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/a5c-ai/babysitter "$T" && mkdir -p ~/.claude/skills && cp -r "$T/library/specializations/domains/science/bioinformatics/skills/salmon-quantifier" ~/.claude/skills/a5c-ai-babysitter-salmon-quantifier && rm -rf "$T"
manifest: library/specializations/domains/science/bioinformatics/skills/salmon-quantifier/SKILL.md
tags
#transcriptomics#quantification#rna-seq#pseudo-alignment#bioinformatics
source content

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)