Phylogenetic tree for covid-19

[karthick1087]

Can we use Snippy for phylogenetic tree construction for COVID-19 from Fastq reads. If not, Can you suggest some tool to work with fastq reads

[andersgs]

@karthick1087 we haven't done too many tests with Snippy. We are using the ARTIC v3 protocol for sequencing (tiled amplicons), for which iVar is better suited as it actually masks the primer sites properly: https://andersen-lab.github.io/ivar/html/manualpage.html

What is your sequencing strategy?