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

in Genome biology by 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

TLDR

  • DEMINERS, a novel DRS toolkit, combines RNA multiplexing, barcode classification, and optimized basecalling to improve accuracy, throughput, and reduce input requirements.

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 mA's role in malaria and glioma. DEMINERS offers a robust, high-throughput solution for precise transcript and RNA modification analysis.

Overview

  • The study presents DEMINERS, a novel toolkit for nanopore direct RNA sequencing (DRS) that aims to increase accuracy, throughput, and reduce input requirements.
  • DEMINERS uses an RNA multiplexing workflow, Random Forest-based barcode classifier, and optimized convolutional neural network basecaller with species-specific training.
  • The primary objective is to develop a robust, high-throughput solution for precise transcript and RNA modification analysis, suitable for various applications like clinical metagenomics, cancer transcriptomics, and parallel transcriptomic comparisons.

Comparative Analysis & Findings

  • DEMINERS enables accurate demultiplexing of up to 24 samples, reducing RNA input and runtime compared to existing DRS tools.
  • The study showcases the toolkit's applications in identifying microbial diversity in COVID-19 patients and exploring the role of mA in malaria and glioma.
  • DEMINERS' optimized basecaller and barcode classifier improve accuracy and throughput, making it a valuable tool for transcript and RNA modification analysis.

Implications and Future Directions

  • The development of DEMINERS offers a promising solution for precise transcript and RNA modification analysis, with potential applications in various fields of research and clinical practice.
  • Future studies can expand on DEMINERS' capabilities by exploring its use in other applications, such as disease diagnosis, pharmacogenomics, and microbiome analysis.
  • Ongoing improvement and optimization of DEMINERS will be necessary to ensure its continued competitiveness with other DRS tools and to address potential limitations or biases.
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