Here a bioinformatic pipeline VVV has been developed to analyse viral populations in a given sample from Next Generation Sequencing (NGS) data. To date, handling large amounts of data from NGS requires the expertise of bioinformaticians, both for data processing and result analysis. Consequently, VVV was designed to help non-bioinformaticians to perform these tasks. By providing only the NGS data file, the developed pipeline generated consensus sequences and determined the composition of the viral population for an avian Metapneumovirus (AMPV) and three different animal coronaviruses (Porcine Epidemic Diarrhea Virus (PEDV), Turkey Coronavirus (TCoV) and Infectious Bronchitis Virus (IBV)). In all cases, the pipeline produced viral consensus genomes corresponding to known consensus sequence and made it possible to highlight the presence of viral genetic variants through a single graphic representation. The method was validated by comparing the viral populations of an AMPV field sample, and of a copy of this virus produced from a DNA clone. VVV demonstrated that the cloned virus population was homogeneous (as designed) at position 2934 where the wild-type virus demonstrated two variant populations at a ratio of almost 50:50. A total of 18, 10, 3 and 28, viral genetic variants were detected for AMPV, PEDV, TCoV and IBV respectively. The simplicity of this pipeline makes the study of viral genetic variants more accessible to a wide variety of biologists, which should ultimately increase the rate of understanding of the mechanisms of viral genetic evolution.

在这里，已经开发了一种生物信息学管道VVV，用于分析来自下一代测序（NGS）数据的给定样本中的病毒种群。迄今为止，处理来自NGS的大量数据需要生物信息学家的专业知识，包括数据处理和结果分析。因此，VVV旨在帮助非生物信息学家执行这些任务。通过仅提供NGS数据文件，开发的管道生成了共识序列，并确定了禽偏肺病毒（AMPV）和三种不同的动物冠状病毒（猪流行性腹泻病毒（PEDV），土耳其冠状病毒（TCoV）和传染性病毒）的病毒种群组成支气管炎病毒（IBV））。在所有情况下，该管道产生了与已知共有序列相对应的病毒共有基因组，并有可能通过单个图形表示突出显示病毒遗传变异体的存在。通过比较AMPV田间样品的病毒种群和从DNA克隆产生的该病毒拷贝的病毒种群，验证了该方法的有效性。VVV证明克隆的病毒群体在2934位是同质的（按设计），其中野生型病毒以接近50:50的比例展示了两个变异群体。分别检测到AMPV，PEDV，TCoV和IBV的总共18、10、3和28个病毒遗传变异。该流程的简单性使各种生物学家更容易进行病毒遗传变异的研究，