SARS-Cov-2 genomics analysis

Question

[kimmitzka]

Hello everyone,

I want to analyse the SARS-Cov-2 genomics. But for the amplicon-based method, is it necessary to know the primer sequence for each sample, no matter whether it is done by Illumina or nanopore? Thanks

[Friederike]

From your question, it is not clear (a) what you have done [and possibly hit an error] and (b) what type of analysis you want to achieve

Answer 1

[Arup Ghosh]

Most of the library preparation kits the ARTIC primer sets and to remove any artifacts introduced by the non-genomic sequences trimming of respective primer sequences is essential for any kind of amplicon sequencing.

Mask or trim primer sequences in Amplicon sequencing