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/

41 SARS-CoV-2 Phylogenomics questions answered

Microbial Bioinformatics is a rapidly changing field marrying computer science and microbiology. Join us as we share some tips and tricks we’ve learnt over the years. If you’re student just getting to grips to the field, or someone who just wants to keep tabs on the latest and greatest - this podcast is for you. 

The hosts are Dr. Lee Katz from the Centres for Disease Control and Prevention (US), Dr. Nabil-Fareed Alikhan from the University of Oxford (UK), and Prof. Andrew Page from Theiagen Genomics (UK) and bring together years of experience in microbial bioinformatics.

The opinions expressed here are our own and do not necessarily reflect the views of Centres for Disease Control and Prevention, University of Oxford or Theiagen Genomics.

Intro music : Werq - Kevin MacLeod (incompetech.com)
Licensed under Creative Commons: By Attribution 3.0 License
http://creativecommons.org/licenses/by/3.0/

Outro music : Scheming Weasel (faster version) - Kevin MacLeod (incompetech.com)
Licensed under Creative Commons: By Attribution 3.0 License
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41 SARS-CoV-2 Phylogenomics questions answered

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