Key result
A complete analysis pipeline and guide was developed to explore sub-consensus variability and reconstruct viral quasispecies from Illumina sequencing data for FMDV and other RNA viruses.
Why the study?
Analyzing next-generation sequencing data to study viral quasispecies can be challenging for inexperienced researchers, creating a need for an accessible analysis guide.
Provides a beginner-friendly bioinformatics pipeline for analyzing viral quasispecies using next-generation sequencing data.
Enables accessible quasispecies analysis for RNA virus research; leaves open clinical integration pending validation.
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.
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Cacciabue et al. (2019) studied Foot-and-mouth disease viruses (FMDV) quasispecies. Next-generation sequencing analysis pipeline was evaluated. A complete analysis pipeline and guide was developed to explore sub-consensus variability and reconstruct viral quasispecies from Illumina sequencing data for FMDV and other RNA viruses.
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