Pangolin Web Application Documenation
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
Assign a lineage to one or more COVID-19 sequences as follow
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.
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
On completion the lineage assignment and two measures of confidence in the assignment (Bootstrap and SH-aLRT values) will be displayed
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.
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'
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
