DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-03-28 DOI:10.1186/s13059-025-03536-3

Junwei Song, Li-an Lin, Chao Tang, Chuan Chen, Qingxin Yang, Dan Zhang, Yuancun Zhao, Han-cheng Wei, Kepan Linghu, Zijie Xu, Tingfeng Chen, Zhifeng He, Defu Liu, Yu Zhong, Weizhen Zhu, Wanqin Zeng, Li Chen, Guiqin Song, Mutian Chen, Juan Jiang, Juan Zhou, Jing Wang, Bojiang Chen, Binwu Ying, Yuan Wang, Jia Geng, Jing-wen Lin, Lu Chen

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引用次数: 0

Abstract

Nanopore direct RNA sequencing (DRS) is a powerful tool for RNA biology but suffers from low basecalling accuracy, low throughput, and high input requirements. We present DEMINERS, a novel DRS toolkit combining an RNA multiplexing workflow, a Random Forest-based barcode classifier, and an optimized convolutional neural network basecaller with species-specific training. DEMINERS enables accurate demultiplexing of up to 24 samples, reducing RNA input and runtime. Applications include clinical metagenomics, cancer transcriptomics, and parallel transcriptomic comparisons, uncovering microbial diversity in COVID-19 and m6A’s role in malaria and glioma. DEMINERS offers a robust, high-throughput solution for precise transcript and RNA modification analysis.

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通过提高纳米孔直接RNA测序的通量和准确性，DEMINERS可以实现临床宏基因组学和比较转录组学分析

纳米孔直接RNA测序（DRS）是RNA生物学研究的有力工具，但存在碱基调用精度低、通量低和输入要求高等缺点。我们提出了DEMINERS，这是一个新颖的DRS工具包，结合了RNA复用工作流程，基于随机森林的条形码分类器和经过优化的具有物种特异性训练的卷积神经网络基础调用器。DEMINERS能够精确地解复用多达24个样品，减少RNA输入和运行时间。应用包括临床宏基因组学、癌症转录组学和平行转录组学比较，揭示了COVID-19中的微生物多样性以及m6A在疟疾和胶质瘤中的作用。DEMINERS为精确的转录物和RNA修饰分析提供了强大的高通量解决方案。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.