pangolin Command Examples

Implements the dynamic nomenclature of SARS-CoV-2 lineages (Pango nomenclature). More information: https://cov-lineages.org/resources/pangolin/usage.html.

• Run pangolin on the specified FASTA file:

pangolin {{path/to/file.fa}}

• Use the specified analysis engine:

pangolin --analysis-mode {{accurate|fast|pangolearn|usher}}