Pangolin

SARS-CoV-2 lineage assignment tool

About

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.

Method

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.

Viewing the output in Pathogenwatch

Downloads, genome reports, and collections

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.

Browsing lineages

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.

How to cite

O'Toole Á, Scher E, Underwood A, et al. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evol. 2021;7(2):veab064. Published 2021 Jul 30. doi:10.1093/ve/veab064