Inclusivity Analysis SARS-CoV2

Question

[akitz]

Hi!

I need to perform a Inclusivity analysis for qPCR primer homology on SARS-CoV2 sequences, mostly for the sequences available through GISAID. I figured out how to blast the primer sequences to the Covid sequences in the NCBI database but the GISAID doesn't have a function like that? I'm willing to dive into R and python options if that's the solution here but I couldn't find anything that would help me out. Can anyone point me towards a package or protocol on how to do this kind of analysis?

Thanks!

[GenoMax]

Assuming you have downloaded GSAID data you could use one of these packages to do a local Primer-Blast like analysis: Automated Primer-Blast like funcionnality