Questions sample prep for virus genotyping sequencing

[Juergen F]

Hi,

Questions:

0 – How do I guarantee a certain # of redundant reads per virus target gene area to be utilized later in assembly?

1 - I assume I would need a virus extraction method (Qiagen, Roche) performed upfront prior starting e.g. an Illumina multiplexing workflow with library prep?

2 - Which sample prep methods do match the input bp size requirements best (... output bp size of sample preps)?

3 - What input virus concentration (copies/ IU) do I need to start e.g. the Illumina multiplexing workflow?

Thanks & Greetings
Juergen