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 some important options
  • What’s this LIBTYPE?
  • Output
  • Misc
  • References
• Salmon Output File Formats
  • Quantification File
  • Command Information File
  • Auxiliary Files
• Fragment Library Types
• License

Indices and tables

• Index

• Module Index

• Search Page