SARS-CoV-2 lineage assignment tool
Pangolin (Phylogenetic Assignment of Named Global Outbreak LINeages) is a tool provided by the Rambaut group as part of the COG-UK consortium for the assignment of lineage names to SARS-CoV-2 genomes.
Pangolin uses an internal machine learning-based method called Pangolearn to assign a lineage to query genomes. For a full description of how lineages are assigned see the description of Pangolearn: https://github.com/cov-lineages/pangolin#pangolearn-description.
The complete output is provided by the CSV download menu in the Genome Browser and the Collection View. It is also shown in the Genome Reports for SARS-CoV-2 genomes (below) along with links to external descriptions of the lineages.
Header and Typing section of a SARS-CoV-2 genome report.
Pangolin lineages are displayed next to SARS-CoV-2 genomes in the Genome Browser and in the Typing table of collections. It's also possible to find genomes with a particular lineage in the Genome Browser by selecting "Betacoronavirus" in the "Genus" filter, "Severe acute respiratory virus" in the "Species" filter, and then "subsp. SARS-CoV-2". This enables the "Lineage" filter, allowing genomes from particular lineages to be selected.
Selecting the B.1.177 lineage.