WarpDemuX-tRNA: barcode multiplexing for nanopore tRNA sequencing
Transfer RNA (tRNA) plays an essential role in protein translation, and tRNA modifications are important to their function. Recently, nanopore direct RNA sequencing (dRNA-seq) has shown promising results in the detection of complex tRNA modifications. However, its wider adoption in the tRNA field ha...
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| Hauptverfasser: | , , , , |
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| Dokumenttyp: | Article (Journal) |
| Sprache: | Englisch |
| Veröffentlicht: |
23 September 2025
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| In: |
Nucleic acids research
Year: 2025, Jahrgang: 53, Heft: 17, Pages: 1-10 |
| ISSN: | 1362-4962 |
| DOI: | 10.1093/nar/gkaf873 |
| Online-Zugang: | Verlag, kostenfrei, Volltext: https://doi.org/10.1093/nar/gkaf873 Verlag, kostenfrei, Volltext: https://academic.oup.com/nar/article/53/17/gkaf873/8250472 
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| Verfasserangaben: | Wiep van der Toorn, Isabel S. Naarmann-de Vries, Wang Liu-Wei, Christoph Dieterich, Max von Kleist |
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| 520 | |a Transfer RNA (tRNA) plays an essential role in protein translation, and tRNA modifications are important to their function. Recently, nanopore direct RNA sequencing (dRNA-seq) has shown promising results in the detection of complex tRNA modifications. However, its wider adoption in the tRNA field has been limited by a lack of (de)multiplexing solutions. Here, we present WarpDemuX-tRNA: an extension to the WarpDemuX method specifically optimized for multiplexed nanopore tRNA sequencing. Using consensus-based signal analysis using (soft) dynamic time warping and barycenter averaging, our approach improves barcode feature generation and achieves more robust barcode identification. WarpDemuX-tRNA outperforms the original method and achieves 99% precision and 95% recovery for four barcodes, while reducing computational complexity and runtime to 6 min per one million reads. WarpDemuX-tRNA is an open-source and free-to-use solution to high-throughput nanopore tRNA sequencing, facilitating more accessible, cost-effective, and high-throughput studies of tRNA modifications and their regulatory mechanisms. | ||
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| 700 | 1 | |a von Kleist, Max |e VerfasserIn |4 aut | |
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