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Nabil-Fareed Alikhan

MicroBinfie Podcast, 41 SARS-CoV-2 Phylogenomics questions answered

microbinfie, podcast1 min read

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/