QutRNA2: robust tRNA modification discovery from Nanopore direct tRNA sequencing.

IF 3 Q1 GENETICS & HEREDITY

NAR Genomics and Bioinformatics Pub Date : 2026-07-07 eCollection Date: 2026-09-01 DOI:10.1093/nargab/lqag065

Michael Piechotta, Wei Guo, Isabel S Naarmann-de Vries, Felix Kallenborn, Swastik Mishra, Francesca Tuorto, Bertil Schmidt, Christoph Dieterich

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Abstract

Transfer RNAs (tRNAs) are essential for protein synthesis and are extensively modified to ensure their structure and function. Direct RNA sequencing with Oxford Nanopore Technologies enables positional modification analysis but is challenged by tRNAs' short length, redundancy, and dense modifications. We present QutRNA2, a scalable workflow that includes GPU-accelerated local alignment, statistical filtering, pairwise error profile comparison, and customizable visualization. Achieving up to 25-fold speed gains over CPU methods, QutRNA2 identifies enzyme-dependent modifications in nuclear- and mitochondrial-encoded tRNAs, demonstrated in high-volume human and mouse samples. This open-source solution provides a comprehensive, multiplexing-compatible framework for tRNA analysis, addressing a key gap in current tools. QutRNA2 is released under Apache-2.0 license and is available at https://github.com/dieterich-lab/QutRNA2.

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QutRNA2：通过纳米孔直接tRNA测序发现强大的tRNA修饰。

转运rna （trna）在蛋白质合成中是必不可少的，并被广泛修饰以确保其结构和功能。直接RNA测序与牛津纳米孔技术实现位置修饰分析，但trna的短长度，冗余和密集修饰的挑战。我们提出了QutRNA2，一个可扩展的工作流，包括gpu加速的局部对齐，统计过滤，成对错误配置文件比较和可定制的可视化。与CPU方法相比，QutRNA2的速度提高了25倍，可识别核和线粒体编码trna中的酶依赖性修饰，这在大量人类和小鼠样本中得到了证明。这个开源解决方案为tRNA分析提供了一个全面的、多路兼容的框架，解决了当前工具中的一个关键空白。QutRNA2在Apache-2.0许可下发布，可从https://github.com/dieterich-lab/QutRNA2获得。

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