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bioRxiv · 10.1101/2025.03.21.644602

WarpDemuX-tRNA: barcode multiplexing for nanopore tRNA sequencing

van der Toorn, W.·Naarmann-de Vries, I. S.·Liu-Wei, W.·Dieterich, C.·von Kleist, M.
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Abstract

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 six minutes 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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van der Toorn, W., Naarmann-de Vries, I. S., Liu-Wei, W., Dieterich, C., von Kleist, M.. 2025-03-23. WarpDemuX-tRNA: barcode multiplexing for nanopore tRNA sequencing. https://doi.org/10.1101/2025.03.21.644602

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