---
name: salmon-quantifier
description: Salmon pseudo-alignment skill for fast and accurate transcript quantification
allowed-tools:
  - Read
  - Write
  - Glob
  - Grep
  - Edit
  - WebFetch
  - WebSearch
  - Bash
metadata:
  version: "1.0"
  category: bioinformatics
  tags:
    - transcriptomics
    - quantification
    - rna-seq
    - pseudo-alignment
graph:
  domains: [domain:bioinformatics]
  specializations: [specialization:biomedical-informatics]
  skillAreas: [skill-area:statistical-analysis, skill-area:python-data-pipelines, skill-area:data-analysis]
  workflows: [workflow:experiment-design]
  roles: [role:research-engineer, role:biomedical-engineer]
---

# 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)


---
Source attribution: a5c-ai
Original project: https://github.com/a5c-ai/babysitter
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Mega AI Hub.

## Upstream license notice

MIT License

Copyright (c) 2026 Gabriel Moreira

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Mega AI Hub resource metadata

Creator / publisher: a5c-ai
Original project: https://github.com/a5c-ai/babysitter
Attribution basis: Upstream repository explicitly recorded in package mirror path

Fields of work: Data & Analytics, Education & Research, Healthcare & Life Sciences, Product Management
Roles: Business Intelligence Analyst, Clinical Research, Data Scientist, Product Manager, Researcher
Specialties: Specialty not specified
Tools: Kallisto, Rsem, Salmon
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: aef1896509dcfa15ca54f4346a268a7a09dadb31413ba7ba8227c51f22b01327