Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis.
Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis.
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DOI：
10.12688/f1000research.10571.1
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发表时间：
2017-01-01
期刊：
影响因子：
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通讯作者：
Au, Kin Fai
中科院分区：
文献类型：
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作者：
Weirather, Jason L;de Cesare, Mariateresa;Au, Kin Fai
背景资料：鉴于第三代测序[Pacific Biosciences（PacBio）和Oxford Nanopore Technologies（ONT）]长读段在许多研究中的实用性，对其数据质量和应用的全面分析和比较是非常必要的。研究方法：基于人类胚胎干细胞的转录组测序数据，我们分析了PacBio和ONT的多个数据特征，包括错误模式，长度，可映射性和相对于先前平台的技术改进。我们还通过比较PacBio、ONT及其相应的Hybrid-Seq策略（PacBio+Illumina和ONT+Illumina）的性能，评估了它们在转录组分析中的应用，例如亚型鉴定和转录组复杂性的定量和表征。结果：PacBio显示出整体更好的数据质量，而ONT提供了更高的产量。与数据质量一样，PacBio在转录组分析中的长读段和Hybrid-Seq策略的大多数方面都略优于ONT。此外，Hybrid-Seq在大多数转录组分析中仅在长读段上显示出上级性能。结论：PacBio和ONT测序均适用于全长单分子转录组分析。正如在Hybrid-Seq分析中首次使用ONT读取所显示的那样，PacBio和ONT都可以从组合的Illumina策略中受益。这里开发的工具和分析方法为这些快速变化的技术的未来应用和评估提供了资源。
Background: Given the demonstrated utility of Third Generation Sequencing [Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT)] long reads in many studies, a comprehensive analysis and comparison of their data quality and applications is in high demand. Methods: Based on the transcriptome sequencing data from human embryonic stem cells, we analyzed multiple data features of PacBio and ONT, including error pattern, length, mappability and technical improvements over previous platforms. We also evaluated their application to transcriptome analyses, such as isoform identification and quantification and characterization of transcriptome complexity, by comparing the performance of PacBio, ONT and their corresponding Hybrid-Seq strategies (PacBio+Illumina and ONT+Illumina). Results: PacBio shows overall better data quality, while ONT provides a higher yield. As with data quality, PacBio performs marginally better than ONT in most aspects for both long reads only and Hybrid-Seq strategies in transcriptome analysis. In addition, Hybrid-Seq shows superior performance over long reads only in most transcriptome analyses. Conclusions: Both PacBio and ONT sequencing are suitable for full-length single-molecule transcriptome analysis. As this first use of ONT reads in a Hybrid-Seq analysis has shown, both PacBio and ONT can benefit from a combined Illumina strategy. The tools and analytical methods developed here provide a resource for future applications and evaluations of these rapidly-changing technologies.