I would like to do a deep mutational scan of a 1kb bacterial protein. I plan to randomly introduce SNPs with error prone PCR. Then, I will apply a selection filter to evaluate fitness of the variants. My question is regarding sequencing of the resulting pools.
Is it possible to evaluate SNPs from short-read sequencing? (I am worried about the assembly of very similar reads). Or should I introduce a barcode to the variants, link barcodes and SNPs via long-read sequencing, and then sequence barcodes via short-read sequencing to determine the selection?