Pangolin Web Application Documenation

Pangolin COVID-19 Lineage Assigner

Phylogenetic Assignment of Named Global Outbreak LINeages

This Web Application assigns lineages to COVID-19 sequences based on the methodology described in this article.

The application uses the software Pangolin developed by Áine O'Toole, JT McCrone, Verity Hill and Andrew Rambaut. The source code can be found here

The source code for the web application can be found here Any issues with the application should be raised on the issue page

How to use

Assign a lineage to one or more COVID-19 sequences as follow

1) Upload one or more COVID-19 sequences by

a) dragging and dropping a (multi)fasta file of sequences onto the 'Drop Zone'

b) Clicking “Select a fasta file to upload” and selecting a (multi)fasta file of sequences.

2) Start Analysis

The uploaded sequences will be in the 'Ready for Analysis' state until you click on the 'Start analysis' button

The sequences will be uploaded and analysis will be started on the web server

3) Review results

On completion the lineage assignment a measure of the likelihood of the assignment will be displayed in the column marked 'Assignment probability'. This is the assignment probability from the trained regression model, the probability of that sequence being the assigned lineage vs any other lineage.

Extra information about the lineage to which the sample has been assigned can be obtained by clicking on the tick button next to the sample

4) Visualise the geographical and temporal distribution in Microreact

Next to each lineage assignment are 2 icons. Clicking on the globe icon will open an interactive Microreact visualisation that shows the lineage selected in the context of global SARS-CoV-2 samples.

Clicking on the UK icon will open an interactive Microreact visualisation that shows the lineage selected in the context of the global SARS-CoV-2 sample collection but filtered for samples of UK origin

For further instructions on how to use Microreact see this introductory video and instructions.

5) Upload another sequence file (Optional)

You can optionally analyse another file of COVID-19 sequences by clicking on the 'Upload another file' button, selecting a file and clicking on 'Start analysis again'

6) Download results

The results can be downloaded in CSV format

If you need to reset the analysis at any time, just click on the 'Reset entries' button