Applications of High-Fidelity Sequencing Protocol to RNA Viruses

Serghei Mangul, Nicholas C. Wu, Ekaterina Nenastyeva, Nicholas Mancuso, Alexander Zelikovsky, Ren Sun, Eleazar Eskin

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

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.

Original languageEnglish (US)
Title of host publicationComputational Methods for Next Generation Sequencing Data Analysis
PublisherWiley
Pages85-104
Number of pages20
ISBN (Electronic)9781119272182
ISBN (Print)9781118169483
DOIs
StatePublished - Sep 6 2016
Externally publishedYes

Keywords

  • High-fidelity sequencing protocol
  • Next-generation sequencing
  • Post-sequencing error correction techniques
  • QuasiRecomb
  • Real HIV data
  • RNA viruses
  • Viral genome assembly

ASJC Scopus subject areas

  • Computer Science(all)

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