47 SARS-CoV-2 Rapid roundup and questions answered

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