Quantifying the limits of accurate and reproducible SNP frequency estimates for influenza within-host sequencing
vRNA was extracted with the RNeasy Mini Kit and cDNA synthesis was performed by random hexamer priming with the Superscript II Double-stranded cDNA synthesis kit. Cleaned cDNA product was used as input for the Nextera XT library preparation kit and products were sequenced with a 600 cycle v2 kit on the Illumina MiSeq.