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Usage:

  • Installation
  • freyja demix
  • freyja variants
  • freyja barcode-build
  • freyja get-lineage-def
  • freyja update
  • freyja boot
  • freyja aggregate
  • freyja plot
  • freyja dash
  • freyja relgrowthrate
  • freyja extract
  • freyja filter
  • freyja covariants
  • freyja plot-covariants

Wiki:

  • Command Line Workflow
  • Cryptic Variant Detection
  • Custom Plotting Tutorial
  • Running Freyja on other pathogens - Measles
  • Demix output manipulation and plotting using R
  • Lineage Barcode Extract
  • Read Analysis Tutorial
  • Terra Workflow
  • Running Freyja on other pathogens
  • Creating custom barcodes
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