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.
复制标题
Pacific Biosciences 和 Oxford Nanopore Technologies 的综合比较及其在转录组分析中的应用[版本 2；
DOI：
10.12688/f1000research.10571.2
复制
发表时间：
2017
期刊：
影响因子：
--
通讯作者：
Au KF
中科院分区：
文献类型：
--
作者：
Weirather JL;de Cesare M;Wang Y;Piazza P;Sebastiano V;Wang XJ;Buck D;Au KF
背景：鉴于第三代测序[太平洋生物科学公司（PacBio）和牛津纳米孔技术公司（ONT）]在许多研究中显示的长读数的效用，对其数据质量和应用的综合分析和比较的需求很高。方法：基于人类胚胎干细胞转录组测序数据，分析PacBio和ONT的多种数据特征，包括错误模式、长度、可映射性和相对于以往平台的技术改进。我们还通过比较大小选择的PacBio、非大小选择的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，如异构体鉴定、转录组复杂性的定量和表征。结果：PacBio整体数据质量更好，ONT产率更高。在数据质量方面，PacBio在转录组分析中的long read - only和Hybrid-Seq策略的大多数方面都略好于ONT。此外，在大多数转录组分析中，Hybrid-Seq仅在长读数上表现出优越的性能。结论：PacBio和ONT测序均适用于全长单分子转录组分析。正如首次在Hybrid-Seq分析中使用ONT reads所显示的那样，PacBio和ONT都可以从Illumina的联合策略中获益。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 size-selected PacBio, non-size-selected 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.