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

47 SARS-CoV-2 Rapid roundup and 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
http://creativecommons.org/licenses/by/3.0/

Question and comments? microbinfie@gmail.com

47 SARS-CoV-2 Rapid roundup and questions answered

Micro Binfie Podcast