DIAGNOSTIC CHALLENGES. “Characterizing the genetic structure of virus populations remains a fundamental challenge. High-throughput sequencing technologies are capable of generating very large datasets; but distinguishing true genetic variation from sequencing error remains a central problem due to the high average sequencing error rates for NGS and given that even small error probabilities result in a significant number of sequencing errors.”
http://www.sciencedirect.com/science/article/pii/S0042682215001580