ARTICnetwork & CLIMB-BIG-DATA present a panel discussion on SARS-CoV-2 phylogenomics with Nick Loman from the University of Birmingham, Verity Hill from the University of Edinburgh, Andrew Page from the Quadram Institute and Anna Price from MRC CLIMB and Cardiff University. This was part of a workshop on COVID-19 data analysis.

The topics covered are:

More about Polecat

Whats the difference between COG-UK Phylotypes and Pangolin lineages?

What is the difference between Civet and Llama

Can you use BLAST to find similar SARS-CoV-2 genomes?

How do you find similar sequences in the public repositories to give your samples context?

How do you manually curate the dataset for PangoLEARN?

How does Civet choose what constitutes a subtree?

Can Civet be adapted to other viruses?

Are the vaccine sequences available?

Databases that report variation

Quality of variant calls?

Groups:

https://www.climb.ac.uk/artic-and-climb-big-data-joint-workshop/

https://www.climb.ac.uk/

https://artic.network/

https://cogconsortium.uk/

Software:

https://github.com/COG-UK/polecat

https://github.com/cov-lineages/pangolin

https://github.com/cov-lineages/llama

https://github.com/artic-network/civet

https://github.com/cov-lineages/pangoLEARN

http://tree.bio.ed.ac.uk/software/figtree/

Analysis websites:

https://cov-lineages.org/

https://clades.nextstrain.org/

https://pangolin.cog-uk.io/

http://cov-glue.cvr.gla.ac.uk/