SARS-CoV-2 Workflow
version v13
Tutorials
Introduction
Setup and installation
Run using example data
Run using custom data
Run using a genomic surveillance configuration
Next steps
Video tutorial walkthrough
Visualization & Interpretation
Visualizing and sharing results
Guidance for interpretation
Nextstrain Narratives
Guides
Update the workflow
Data preparation guide
Prepare your own local data
Curate data from GISAID search and downloads
Curate data from the full GISAID database
Workflow config file guide
Customizing visualization
Run the workflow on Terra
Reference
Nextstrain overview
Files overview
Workflow config file reference
Remote inputs
Standard metadata fields
Clade Naming & Definitions
Data Submitter’s FAQ
Troubleshoot common issues
Change Log
Glossary
Stuck? Ask us on the discussion board. We're happy to help!
SARS-CoV-2 Workflow
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SARS-CoV-2 Workflow
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A
|
C
|
D
|
N
|
S
A
analysis directory
Auspice config file
C
config file
customization file
D
default files
N
ncov workflow
S
Snakemake
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v: v13
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