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

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机构： [1]Department of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu 610041, China. [2]Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China [3]Biosafety Laboratory, lnternational Center for Biological and Translational Research, West China Hospital, Sichuan University, Chengdu 610041, China. [4]School of Pharmacy, School of Basic Medical Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China [5]Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu 610041, China [6]Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu 610041, China.

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关键词： Nanopore direct RNA sequencing Demultiplex Basecalling RNA modification Machine learning

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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.© 2025. The Author(s).

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出版当年[2025]版：

大类 | 1 区

生物学

小类 | 1 区生物工程与应用微生物 1 区遗传学

最新[2025]版：

大类 | 1 区

生物学

小类 | 1 区生物工程与应用微生物 1 区遗传学

第一作者：

第一作者机构： [1]Department of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu 610041, China.

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通讯机构： [2]Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China [3]Biosafety Laboratory, lnternational Center for Biological and Translational Research, West China Hospital, Sichuan University, Chengdu 610041, China.

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