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