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

被引：0

作者：

Song, Junwei ^{[1
]}

Lin, Li-an ^{[1
]}

Tang, Chao ^{[1
,5
]}

Chen, Chuan ^{[2
,3
,4
,6
]}

Yang, Qingxin ^{[1
]}

Zhang, Dan ^{[1
]}

Zhao, Yuancun ^{[1
]}

Wei, Han-cheng ^{[2
,3
,4
,5
]}

Linghu, Kepan ^{[1
]}

Xu, Zijie ^{[1
]}

Chen, Tingfeng ^{[1
]}

He, Zhifeng ^{[1
]}

Liu, Defu ^{[1
]}

Zhong, Yu ^{[5
]}

Zhu, Weizhen ^{[8
]}

Zeng, Wanqin ^{[1
]}

Chen, Li ^{[1
]}

Song, Guiqin ^{[6
]}

Chen, Mutian ^{[2
,3
,4
]}

Jiang, Juan ^{[7
]}

Zhou, Juan ^{[2
,3
,4
]}

Wang, Jing ^{[7
]}

Chen, Bojiang ^{[7
]}

Ying, Binwu ^{[2
,3
,4
]}

Wang, Yuan ^{[2
,3
,4
]}

Geng, Jia ^{[2
,3
,4
]}

Lin, Jing-wen ^{[2
,3
,4
,5
]}

Chen, Lu ^{[1
]}

机构：

[1] Sichuan Univ, West China Univ Hosp 2, Key Lab Birth Defects & Related Dis Women & Childr, Dept Lab Med,State Key Lab Biotherapy, Chengdu 610041, Peoples R China

[2] Sichuan Univ, West China Hosp, State Key Lab Biotherapy, Dept Lab Med, Chengdu 610041, Peoples R China

[3] Sichuan Univ, West China Hosp, Canc Ctr, Chengdu 610041, Peoples R China

[4] Collaborat Innovat Ctr, Chengdu 610041, Peoples R China

[5] Sichuan Univ, West China Hosp, lnternat Ctr Biol & Translat Res, Biosafety Lab, Chengdu 610041, Peoples R China

[6] North Sichuan Med Coll, Sch Pharm, Sch Basic Med Sci & Forens Med, Nanchong 637000, Peoples R China

[7] Sichuan Univ, West China Hosp, Precis Med Ctr, Precis Med Key Lab Sichuan Prov, Chengdu 610041, Peoples R China

[8] Sichuan Univ, West China Hosp, Inst Urol, Dept Urol, Chengdu 610041, Peoples R China

来源：

GENOME BIOLOGY | 2025年 / 26卷 / 01期

基金：

中国国家自然科学基金; 中国博士后科学基金;

关键词：

Nanopore direct RNA sequencing; Demultiplex; Basecalling; RNA modification; Machine learning; M(6)A MODIFICATION;

D O I：

10.1186/s13059-025-03536-3

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：34

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