Identify a SARS-CoV2 strain

1

Hi guys,

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

2

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

3

Thank you for the reply.