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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: van der Toorn, Wiep (VerfasserIn) , Naarmann-de Vries, Isabel S. (VerfasserIn) , Liu-Wei, Wang (VerfasserIn) , Dieterich, Christoph (VerfasserIn) , von Kleist, Max (VerfasserIn)
Dokumenttyp: Article (Journal)
Sprache:Englisch
Veröffentlicht: 23 September 2025
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
Volltext
Verfasserangaben:Wiep van der Toorn, Isabel S. Naarmann-de Vries, Wang Liu-Wei, Christoph Dieterich, Max von Kleist
Beschreibung
Zusammenfassung: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.
Beschreibung:Online veröffentlicht: 10. September 2025
Gesehen am 23.10.2025
Beschreibung:Online Resource
ISSN:1362-4962
DOI:10.1093/nar/gkaf873

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