We discuss the latest developments in SARS-CoV-2 genomics over the last 2 weeks with Mads Albertsen and the latest developments in Denmark.

Denmark covid stats: www.covid19genomics.dk/statistics

Tools and resources mentioned:

https://outbreak.info/

https://virological.org/t/outbreak-info-sars-cov-2-mutation-situation-reports/629

https://gitlab.com/johan.bernal.morales/sarscov2

Publications mentioned:

A Comparison of Performance for Different SARS-Cov-2 Sequencing Protocols https://www.biorxiv.org/content/10.1101/2021.03.01.433428v1

Before the Surge: Molecular Evidence of SARS-CoV-2 in New York City Prior to the First Report

https://www.medrxiv.org/content/10.1101/2021.02.08.21251303v1

SARS-CoV-2 within-host diversity and transmission https://science.sciencemag.org/content/early/2021/03/09/science.abg0821

Info on masking SARSCOV2 sites:

https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473

https://github.com/W-L/ProblematicSites_SARS-CoV2/blob/master/subset_vcf/problematic_sites_sarsCov2.mask.vcf