Abstract

Deep sequencing of viral populations using next-generation sequencing (NGS) offers opportunities to understand and investigate evolution, transmission dynamics, and population genetics. Currently, the standard practice for processing NGS data to study viral populations is to summarize all the observed sequences from a sample as a single consensus sequence, thus discarding valuable information about the intrahost viral molecular epidemiology. Furthermore, existing analytical pipelines may only analyze genomic regions involved in drug resistance, thus are not suited for full viral genome analysis. Here, we present HAPHPIPE, a HAplotype and PHylodynamics PIPEline for genome-wide assembly of viral consensus sequences and haplotypes. The HAPHPIPE protocol includes modules for quality trimming, error correction, de novo assembly, alignment, and haplotype reconstruction. The resulting consensus sequences, haplotypes, and alignments can be further analyzed using a variety of phylogenetic and population genetic software. HAPHPIPE is designed to provide users with a single pipeline to rapidly analyze sequences from viral populations generated from NGS platforms and provide quality output properly formatted for downstream evolutionary analyses.

中文翻译：

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HAPHPIPE：用于宿主内病毒种群深度测序的单倍型重建和系统动力学

摘要

使用下一代测序（NGS）对病毒种群进行深度测序提供了理解和研究进化，传播动力学和种群遗传学的机会。当前，处理NGS数据以研究病毒种群的标准做法是将样本中观察到的所有序列汇总为单个共有序列，从而丢弃有关宿主内病毒分子流行病学的有价值的信息。此外，现有的分析管线可能仅分析与药物抗性有关的基因组区域，因此不适合进行完整的病毒基因组分析。在这里，我们介绍HAPHPIPE，HAploipe和系统动力学PIPEline，用于病毒共有序列和单倍型的全基因组组装。HAPHPIPE协议包括用于质量修整，纠错，从头组装，对齐，和单倍型重建。可以使用多种系统发育和群体遗传软件对所得的共有序列，单倍型和比对进行进一步分析。HAPHPIPE旨在为用户提供单一流水线，以快速分析NGS平台生成的病毒种群的序列，并提供正确格式化的高质量输出以用于下游进化分析。