A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing

CACCIABUE, MARCO; KÖNIG, GUIDO; CARRILLO, ELISA; CURRÁ, ANABELLA; GISMONDI, MARÍA INÉS

BRIEFINGS IN BIOINFORMATICS

OXFORD UNIV PRESS

Año: 2020 vol. 21 p. 1766 - 1775

1467-5463

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.