Welcome to Salmon’s documentation!

Contents:

• Requirements
  • Binary Releases
  • Requirements for Building from Source
• Installation
• Salmon
  • Using Salmon
  • Preparing transcriptome indices (mapping-based mode)
  • Quantifying in mapping-based mode
  • Quantifying in alignment-based mode
  • Description of important options
  • What’s this LIBTYPE?
  • Output
  • Misc
  • References
• Alevin
  • Using Alevin
  • Providing multiple read files to Alevin
  • Description of important options
  • Output
  • Output Quality Check
  • Tutorial & Parsers
  • Misc
  • BibTex
  • DOI
  • References
• Salmon Output File Formats
  • Quantification File
  • Command Information File
  • Auxiliary Files
• Fragment Library Types

Indices and tables

• Index
• Module Index
• Search Page