Identify a SARS-CoV2 strain

Hi guys,

I have a few contigs that turned out to be SARS-CoV2, how can I identify the strain?

if they are long enough (>1000bp), actually SARS-CoV-2, and of reasonable quality, you should be able to stick them into nextclade to identify the clade. Accurate assignment is often impossible for genome fragments though.

Thank you for the reply.