Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China.
Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China.
Nat Commun. 2024 May 10;15(1):3972. doi: 10.1038/s41467-024-48117-3.
The advancement of Long-Read Sequencing (LRS) techniques has significantly increased the length of sequencing to several kilobases, thereby facilitating the identification of alternative splicing events and isoform expressions. Recently, numerous computational tools for isoform detection using long-read sequencing data have been developed. Nevertheless, there remains a deficiency in comparative studies that systemically evaluate the performance of these tools, which are implemented with different algorithms, under various simulations that encompass potential influencing factors. In this study, we conducted a benchmark analysis of thirteen methods implemented in nine tools capable of identifying isoform structures from long-read RNA-seq data. We evaluated their performances using simulated data, which represented diverse sequencing platforms generated by an in-house simulator, RNA sequins (sequencing spike-ins) data, as well as experimental data. Our findings demonstrate IsoQuant as a highly effective tool for isoform detection with LRS, with Bambu and StringTie2 also exhibiting strong performance. These results offer valuable guidance for future research on alternative splicing analysis and the ongoing improvement of tools for isoform detection using LRS data.
长读测序（Long-Read Sequencing，LRS）技术的进步显著增加了测序的长度至几千个碱基，从而促进了可变剪接事件和异构体表达的鉴定。最近，已经开发出了许多使用长读测序数据进行异构体检测的计算工具。然而，仍然缺乏对这些工具的性能进行系统评估的比较研究，这些工具使用不同的算法，在各种模拟中涵盖了潜在的影响因素。在这项研究中，我们对九个工具中的十三种方法进行了基准分析，这些方法能够从长读 RNA-seq 数据中识别异构体结构。我们使用模拟数据、RNA sequins（测序插入物）数据以及实验数据来评估它们的性能。我们的研究结果表明 IsoQuant 是一种非常有效的 LRS 异构体检测工具，Bambu 和 StringTie2 也表现出很强的性能。这些结果为未来的可变剪接分析研究以及使用 LRS 数据进行异构体检测工具的不断改进提供了有价值的指导。
