metagenlab/diag_pipelines
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Contents:

  • Cookbook
  • Generalities
  • Core genome determination
  • Assembly and quality
  • Virulence
  • Resistance
  • Epidemiology
  • All Deliverables
metagenlab/diag_pipelines
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  • Documentation for the genomics and metagenomics workflows
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Documentation for the genomics and metagenomics workflowsΒΆ

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
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