A beginner's guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing. (1st November 2019)

• Record Type: Journal Article
• Authors: Cacciabue, Marco; Currá, Anabella; Carrillo, Elisa; König, Guido; Gismondi, María Inés
• Is Part Of: Briefings in bioinformatics. Volume 21:Number 5(2020)
• Page Start: 1766
• Page End: 1775
• Publication Date: 2019-11-01
• Subjects: viral quasispecies -- Illumina sequencing platform -- analysis workflow -- open-source software -- sub-consensus SNV -- haplotype reconstruction; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbz086
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: Deep sequencing of viral genomes is a powerful tool to study RNA virus complexity. However, the analysis of next-generation sequencing data might be challenging for researchers who have never approached the study of viral quasispecies by this methodology. In this work we present a suitable and affordable guide to explore the sub-consensus variability and to reconstruct viral quasispecies from Illumina sequencing data. The guide includes a complete analysis pipeline along with user-friendly descriptions of software and file formats. In addition, we assessed the feasibility of the workflow proposed by analyzing a set of foot-and-mouth disease viruses (FMDV) with different degrees of variability. This guide introduces the analysis of quasispecies of FMDV and other viruses through this kind of approach.