Documentation for the genomics and metagenomics workflows

Contents:

• Cookbook
  • Dependencies
  • General use
  • Run one of the 4 workflows
  • Generating specific files of interest
• Generalities
  • Defining variables
  • Configuration file
  • Logging functions
  • Determining sample names
  • Workflows and Rules
• Core genome determination
  • Ridom
  • Enterobase
  • ParSNP
• Assembly and quality
  • Parameters
  • Deliverables
• Virulence
  • Parameters
  • Deliverables
• Resistance
  • Parameters
  • Available softwares
  • Mycobacterium tuberculosis specific analyses
  • Deliverables
• Epidemiology
  • Parameters
  • Available Genotypers
  • Filtering
  • Calculating differences
  • Phylogeny
  • Deliverables
• All Deliverables