We present a rapid round up of SARS-CoV-2 questions and issues, hopefully with some answers, so that you can stay on top of the latest in SARS-CoV-2 genomics. Recorded 5 February 2021.
Topics covered:
Why missing 1 SNP can cause lineage assignment to break and how it works?
How do we describe lineages with a chain of mutation events?
Are we seeing convergent evolution?
Co-infections of different lineages discovered?
For nanopore basecalling do use HAC & should you get a GPU?
Basic logistics difficult for sequencing in many parts of world.
Can I look at recombination with ARTIC on Illumina?
How do you annotate a SARS-CoV-2 sequence?
http://cov-glue.cvr.gla.ac.uk/#/home
FASTA > nextclade
VCF > snpeff
https://github.com/cov-ert/type_variants
Spotting community spread from NextStrain?
Scientists call for fully open sharing of coronavirus genome data: https://www.nature.com/articles/d41586-021-00305-7
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