Institute of Medical Virology, University of Zurich, Switzerland.
PLoS One. 2012;7(10):e47046. doi: 10.1371/journal.pone.0047046. Epub 2012 Oct 3.
Recent advancements of sequencing technology have opened up unprecedented opportunities in many application areas. Virus samples can now be sequenced efficiently with very deep coverage to infer the genetic diversity of the underlying virus populations. Several sequencing platforms with different underlying technologies and performance characteristics are available for viral diversity studies. Here, we investigate how the differences between two common platforms provided by 454/Roche and Illumina affect viral diversity estimation and the reconstruction of viral haplotypes. Using a mixture of ten HIV clones sequenced with both platforms and additional simulation experiments, we assessed the trade-off between sequencing coverage, read length, and error rate. For fixed costs, short Illumina reads can be generated at higher coverage and allow for detecting variants at lower frequencies. They can also be sufficient to assess the diversity of the sample if sequences are dissimilar enough, but, in general, assembly of full-length haplotypes is feasible only with the longer 454/Roche reads. The quantitative comparison highlights the advantages and disadvantages of both platforms and provides guidance for the design of viral diversity studies.
测序技术的最新进展在许多应用领域开辟了前所未有的机会。现在，可以使用非常深的覆盖度有效地对病毒样本进行测序，以推断潜在病毒群体的遗传多样性。有几种具有不同基础技术和性能特征的测序平台可用于病毒多样性研究。在这里，我们研究了 454/Roche 和 Illumina 这两种常见平台之间的差异如何影响病毒多样性估计和病毒单倍型的重建。我们使用两种平台测序的十个 HIV 克隆的混合物和额外的模拟实验，评估了测序覆盖率、读长和错误率之间的权衡。对于固定成本，Illumina 的短读长可以在更高的覆盖度下生成，并允许检测到更低频率的变体。如果序列足够不同，它们也可以足以评估样本的多样性，但通常只有更长的 454/Roche 读长才能组装全长单倍型。定量比较突出了两种平台的优缺点，并为病毒多样性研究的设计提供了指导。
