Tools and Strategies for Long-Read Sequencing and De Novo Assembly of Plant Genomes

用于植物基因组长读测序和从头组装的工具和策略

Highlights 要点

测序成本的大幅下降、生物信息学管道的改善以及高性能计算能力的增强，已经导致了一场完美风暴，在这场风暴中，非专业的基因组研究小组能够访问、部署和生成非模型植物系统中的全新基因组序列。

然而，由于基因组的大小、复杂性以及实验和计算设计，为许多植物物种生成高质量的组装仍然面临着重大的挑战。

为一个新的基因组项目选择最合适的测序和软件平台可能会令人困惑和畏缩，因为在不同的环境中，可用选项的范围很广，而且特定工具的性能质量也不同

The commercial release of third-generation sequencing technologies (TGSTs),giving long and ultra-long sequencing reads, has stimulated the development of new tools for assembling highly contiguous genome sequences with unprecedented accuracy across complex repeat regions.

We survey here a wide range of emerging sequencing platforms and analytical tools for de novo assembly,
provide background information for each of their steps, and discuss the spectrum of available options.

Our decision tree recommends workflows for the generation of a high-quality genome assembly when used in combination with
the specific needs and resources of a project.

第三代测序技术(TGSTs)的商业发布，提供了长和超长的测序解读，刺激了新的工具的发展，以前所未有的准确性装配高度连续的基因组序列，跨越复杂的重复区域。我们在这里调查了一系列新兴的测序平台和分析工具，为de novo装配提供背景信息，并讨论了可用选项的范围。我们的决策树建议在结合项目的特定需求和资源使用时，生成高质量基因组组装的工作流程。

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