Lineages classification using Pangolin

Pangolin (Phylogenetic Assignment of Named Global Outbreak Lineages) is a piece of software created by the same team that proposed the Pango nomenclature scheme, which we discussed earlier in the course. It’s easy to use and allows labs to quickly assign the most likely Pango lineage to newly sequenced data.

Installing is simple for users who are familiar with the UNIX environment, as it only requires a Python interpreter to run Pangolin and the Conda system to install dependencies.

Pangolin is also available as a web-based application for less experienced users. Users can submit SARS-CoV-2 genome sequences in FASTA format by dragging and dropping or selecting from the browser’s file browser. The sequences will be analysed using the Pangolin software after they have been uploaded (versions of the software and the underlying data are displayed at the bottom of the page).

When the processing is complete, the lineage for each sample, as well as the bootstrap support values, are displayed. Links to additional information on the lineage and its visualisation within the Microreact platform are also provided. The results are available as a CSV spreadsheet file download. Almost three million virus genomes have been uploaded to Pangolin’s web application to date, enabling SARS-CoV-2 genomic epidemiology and providing scientists with key information about viral lineage transmission. Complete instructions for using the Pangolin web application and a tutorial for the command-line version is available at Cov-Lineages website.

References

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

Assignment of epidemiological lineages in an emerging pandemic using the Pangolin tool