info:eu-repo/semantics/article
A beginner's guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing
Fecha
2020-09Registro en:
Cacciabue, Marco Polo Domingo; Currá, Anabella Paola; Carrillo, Elisa Cristina; König, Guido Alberto; Gismondi, Maria Ines; A beginner's guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing; Oxford University Press; Briefings In Bioinformatics; 21; 5; 9-2020; 1766–1775
1467-5463
CONICET Digital
CONICET
Autor
Cacciabue, Marco Polo Domingo
Currá, Anabella Paola
Carrillo, Elisa Cristina
König, Guido Alberto
Gismondi, Maria Ines
Resumen
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.