Welcome to Salmon’s documentation!

Contents:

• Requirements
  • Binary Releases
  • Requirements for Building from Source
• Installation
• Using Salmon
• Preparing transcriptome indices (mapping-based mode)
• Quantifying in mapping-based mode
  • Providing multiple read files to Salmon
• Quantifying in alignment-based mode
• Description of important options
  • --validateMappings
  • --mimicBT2
  • --mimicStrictBT2
  • --recoverOrphans
  • --hardFilter
  • --skipQuant
  • --allowDovetail
  • -p / --threads
  • --dumpEq
  • --incompatPrior
  • --fldMean
  • --fldSD
  • --minScoreFraction
  • --bandwidth
  • --maxMMPExtension
  • --ma
  • --mp
  • --go
  • --ge
  • --rangeFactorizationBins
  • --useEM
  • --numBootstraps
  • --numGibbsSamples
  • --seqBias
  • --gcBias
  • --posBias
  • --biasSpeedSamp
  • --writeUnmappedNames
  • --writeMappings
• What’s this LIBTYPE?
• Output
• Misc
• References
• Alevin
  • Using Alevin
  • Providing multiple read files to Alevin
  • Description of important options
  • Output
  • Misc
  • References
• Salmon Output File Formats
  • Quantification File
  • Command Information File
  • Auxiliary Files
• Fragment Library Types

Indices and tables

• Index
• Module Index
• Search Page