Long-read sequencing data analysis for yeasts
Long-read sequencing data analysis for yeasts
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DOI：
10.1038/nprot.2018.025
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发表时间：
2018-06-01
期刊：
影响因子：
14.8
通讯作者：
Liti, Gianni
中科院分区：
文献类型：
--
作者：
Yue, Jia-Xing;Liti, Gianni
长读测序技术因其在解析复杂基因组区域方面的优势而变得越来越受欢迎。酿酒酵母作为一种基因组规模小、具有重大生物技术意义的领先模式生物，目前有许多菌株正在进行长阅读测序。然而，分析长时间阅读的测序数据以产生高质量的基因组组装和注释仍然具有挑战性。在这里，我们提出了一个名为酵母长读测序数据分析(LRSDAY)的模块化计算框架，这是第一个简化这一过程的一站式解决方案。从原始测序读数开始，LRSDAY可以以高度自动化的方式产生染色体水平的基因组组装和全面的基因组注释，只需最少的人工干预，这是迄今为止使用任何替代工具都不可能做到的。注释的基因组特征包括着丝粒、蛋白质编码基因、tRNAs、转座元件(TES)和端粒相关元件。虽然是为酿酒酵母量身定做的，但我们将LRSDAY设计为高度模块化和可定制的，使其几乎适用于任何真核生物。当将LRSDAY应用于酿酒酵母菌株时，从类似于100x太平洋生物科学(PacBio)运行基本工作流程的四个线程生成完整且注释良好的基因组所需时间类似于41小时。对于使用LRSDAY执行分析，建议您具有在Linux命令行环境中工作的基本经验。
Long-read sequencing technologies have become increasingly popular due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast Saccharomyces cerevisiae has many isolates currently being sequenced with long reads. However, analyzing long-read sequencing data to produce high-quality genome assembly and annotation remains challenging. Here, we present a modular computational framework named long-read sequencing data analysis for yeasts (LRSDAY), the first one-stop solution that streamlines this process. Starting from the raw sequencing reads, LRSDAY can produce chromosome-level genome assembly and comprehensive genome annotation in a highly automated manner with minimal manual intervention, which is not possible using any alternative tool available to date. The annotated genomic features include centromeres, protein-coding genes, tRNAs, transposable elements (TEs), and telomere-associated elements. Although tailored for S. cerevisiae, we designed LRSDAY to be highly modular and customizable, making it adaptable to virtually any eukaryotic organism. When applying LRSDAY to an S. cerevisiae strain, it takes similar to 41 h to generate a complete and well-annotated genome from similar to 100x Pacific Biosciences (PacBio) running the basic workflow with four threads. Basic experience working within the Linux command-line environment is recommended for carrying out the analysis using LRSDAY.