Year: 2025
Type: article
Abstract: Nanopore direct RNA sequencing (dRNA-seq) enables unique insights into RNA biology. However, applications are currently limited by the lack of accurate and cost-effective sample multiplexing. Here we introduce WarpDemuX, an ultra-fast and highly accurate adapter-barcoding and demultiplexing approach for dRNA-seq with SQK-RNA002 and SQK-RNA004 chemistries. WarpDemuX enhances speed and accuracy by fast processing of the raw nanopore signal, use of a light-weight machine-learning algorithm and design of optimized barcode sets. We demonstrate its utility by performing rapid phenotypic profiling of different SARS-CoV-2 viruses through multiplexed sequencing of longitudinal samples on a single flowcell, identifying systematic differences in transcript abundance and poly(A) tail lengths during infection. Additionally, integrating WarpDemuX into sequencing control software enables real-time enrichment of target molecules through barcode-specific adaptive sampling, which we demonstrate by enriching low abundance viral RNA. In summary, WarpDemuX represents a broadly applicable, high-performance, economical multiplexing solution for dRNA-seq, facilitating advanced (epi-) transcriptomic research.
Source: Nature Communications
Institutions: Robert Koch Institute, Freie Universität Berlin, Helmholtz Centre for Infection Research, Helmholtz Institute for RNA-based Infection Research, Max Planck Society, Centre National de la Recherche Scientifique, Architecture et Réactivité de l'arN, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, University of Würzburg
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $6,990
Funders: European Commission, Deutsche Forschungsgemeinschaft, Agence Nationale de la Recherche, Institut National de la Santé et de la Recherche Médicale, Bundesministerium für Bildung und Forschung, Université de Strasbourg, Centre National de la Recherche Scientifique, Freie Universität Berlin, National Institute of Allergy and Infectious Diseases, H2020 Marie Skłodowska-Curie Actions
Awards: G1190173965, G1372115314, G164444715, G2033548659, Understanding (harmful) virus-host interactions by linking virology and bioinformatics, Par-delà les frontières, l'Université de Strasbourg, G2255650664, G2659019386, G2694206344, Façonner les talents en formation et en recherche à l'Université de Strasbourg, G2980570810, Understanding (harmful) virus-host interactions by linking virology and bioinformatics, G3357951378, G3730343, G399734812, G434337789, Integrative Molecular and Cellular Biology, G471331628, G4779185514, G6136357505, G6803667113, G7240651115, G7358480839, G7483376350, G7604888570, EXC 2046: MATH+: Berlin Mathematics Research Center, G7802408855, Center for Structural Biology of HIV RNA
OpenAlex ID: W4409647413