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 workflows
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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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