中山大学岳家兴等研究人员合作开发出利用纳米孔直接RNA测序进行转录组综合分析的集成计算框架。相关论文于2024年7月14日在线发表在《遗传学报》上。

研究人员报道了NanoTrans，一个综合计算框架，全面涵盖所有主要的直接RNA测序（DRS）应用范围，包括异构体聚类和量化、多聚腺苷酸尾长估计、RNA修饰分析以及融合基因检测。除了提供这样一个流线型的一站式解决方案的优势外，NanoTrans还以其工作流程导向的模块化设计、批处理能力、全方位的表格和图形报告输出，以及自动安装和配置支持而脱颖而出。

最后，通过将NanoTrans应用于酵母、拟南芥以及人类胚肾和癌细胞系的真实DRS数据集，研究人员进一步展示了其在各种DRS应用环境中的实用性、有效性和效率。

研究人员表示，纳米孔DRS能够直接获取原始RNA链的全长信息，揭示基因表达谱丰富的定性和定量特性。

附：英文原文

Title: NanoTrans: an integrated computational framework for comprehensive transcriptome analysis with Nanopore direct RNA sequencing

Author: Li Zhang a, Jing Li a, Jia-Xing Yue a

Issue&Volume: 2024/07/14

Abstract: Nanopore direct RNA sequencing (DRS) provides the direct access to native RNA strands with full-length information, shedding light on rich qualitative and quantitative properties of gene expression profiles. Here with NanoTrans, we present an integrated computational framework that comprehensively covers all major DRS-based application scopes, including isoform clustering and quantification, poly(A) tail length estimation, RNA modification profiling, and fusion gene detection. In addition to its merit in providing such a streamlined one-stop solution, NanoTrans also shines in its workflow-orientated modular design, batch processing capability, all-in-one tabular and graphic report output, as well as automatic installation and configuration supports. Finally, by applying NanoTrans to real DRS datasets of yeast, Arabidopsis, as well as human embryonic kidney and cancer cell lines, we further demonstrated its utility, effectiveness, and efficacy across a wide range of DRS-based application settings.

DOI: 10.1016/j.jgg.2024.07.007

Source: https://www.sciencedirect.com/science/article/pii/S1673852724001838