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.

译文

:病毒基因组的深度测序是研究RNA病毒复杂性的有力工具。然而,对于从未使用这种方法进行病毒准种研究的研究人员而言,下一代测序数据的分析可能具有挑战性。在这项工作中,我们提供了一个合适且价格合理的指南,以探讨亚共识变异性并从Illumina测序数据重建病毒准种。该指南包括完整的分析流程以及对软件和文件格式的用户友好描述。此外,我们通过分析一组具有不同程度变异性的口蹄疫病毒(FMDV),评估了提出的工作流程的可行性。本指南通过这种方法介绍了对FMDV和其他病毒的准种的分析。

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