Applications of High-Fidelity Sequencing Protocol to RNA Viruses

This chapter describes the used high-fidelity sequencing protocol, and introduces the approach for viral genome assembly (VGA) based on high-fidelity sequencing data. It presents the results of performance of VGA and some other viral assemblers on simulated data, describes the performance of VGA on real HIV data. The chapter compares different aligners to investigate the effect of their alignment on mapping statistics. Post-sequencing error correction techniques are available for reads obtained by regular protocol offering the possibility to partially correct sequencing errors trading off for real biological mutations. HCV virus exhibits more complex genomic architecture with lower population diversity and longer conserved regions than HIV. QuasiRecomb is designed to handle paired-end read data and manages to produce full-length viral genomes. The chapter discusses the application of the high-fidelity protocol that is the evaluation of error correction methods for next-generation sequencing (NGS) reads.