Re. hybrid capture-, shotgun-, and amplicon-based methods for virus (Illumina) sequencing - these are our rule of thumb recommendations for which method to use, given different levels of starting material. All these for consensus sequence generation - iSNVs you need Ct <30.https://twitter.com/K_G_Andersen/status/1083391004185526272 …
Haha, I thought we could squirm our way out of that one 
. But, yes - basically what Nate says: (1) Very expensive, (2) Time consuming, (3) Coverage MUCH lower. Rule of thumb: Ct <25 = metagenomic, 25-30 = hybrid capture, 25-35 = PrimalSeq, >35 = ForgetItSeq.
. But, yes - basically what Nate says: (1) Very expensive, (2) Time consuming, (3) Coverage MUCH lower. Rule of thumb: Ct <25 = metagenomic, 25-30 = hybrid capture, 25-35 = PrimalSeq, >35 = ForgetItSeq.
