Surachat Komwit, Taylor Todd Duane, Wattanamatiphot Wanicbut, Sukpisit Sukgamon, Jeenkeawpiam Kongpop
Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand.
Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand.
Heliyon. 2022 Aug 15;8(8):e10255. doi: 10.1016/j.heliyon.2022.e10255. eCollection 2022 Aug.
RNA-seq is a sequencing technique that uses next-generation sequencing (NGS) to explore and study the entire transcriptome of a biological sample. NGS-based analyses are mostly performed via command-line interfaces, which is an obstacle for molecular biologists and researchers. Therefore, the higher throughputs from NGS can only be accessed with the help of bioinformatics and computer science expertise. As the cost of sequencing is continuously falling, the use of RNA-seq seems certain to increase. To minimize the problems encountered by biologists and researchers in RNA-seq data analysis, we propose an automated platform with a web application that integrates various bioinformatics pipelines. The platform is intended to enable academic users to more easily analyze transcriptome datasets. Our automated Transcriptome Analysis Platform (aTAP) offers comprehensive bioinformatics workflows, including quality control of raw reads, trimming of low-quality reads, de novo transcriptome assembly, transcript expression quantification, differential expression analysis, and transcript annotation. aTAP has a user-friendly graphical interface, allowing researchers to interact with and visualize results in the web browser. This project offers an alternative way to analyze transcriptome data, by integrating efficient and well-known tools, that is simpler and more accessible to research communities. aTAP is freely available to academic users at https://atap.psu.ac.th/.
RNA测序是一种利用新一代测序（NGS）技术来探索和研究生物样本整个转录组的测序技术。基于NGS的分析大多通过命令行界面进行，这对分子生物学家和研究人员来说是一个障碍。因此，只有借助生物信息学和计算机科学专业知识，才能利用NGS更高的通量。随着测序成本不断下降，RNA测序的应用似乎必将增加。为了尽量减少生物学家和研究人员在RNA测序数据分析中遇到的问题，我们提出了一个带有网络应用程序的自动化平台，该平台整合了各种生物信息学流程。该平台旨在使学术用户能够更轻松地分析转录组数据集。我们的自动化转录组分析平台（aTAP）提供全面的生物信息学工作流程，包括原始读数的质量控制、低质量读数的修剪、从头转录组组装、转录本表达定量、差异表达分析和转录本注释。aTAP具有用户友好的图形界面，允许研究人员在网络浏览器中与结果进行交互并可视化。该项目通过整合高效且知名的工具，提供了一种分析转录组数据的替代方法，这种方法对研究群体来说更简单且更容易使用。学术用户可在https://atap.psu.ac.th/免费使用aTAP。
