IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-59102-9.html
   My bibliography  Save this article

Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing

Author

Listed:
  • Wiep Toorn

    (Robert Koch Institute
    Freie Universität Berlin)

  • Patrick Bohn

    (Helmholtz Centre for Infection Research)

  • Wang Liu-Wei

    (Robert Koch Institute
    Freie Universität Berlin
    International Max-Planck Research School for Biology and Computing (IMPRS-BAC))

  • Marco Olguin-Nava

    (Helmholtz Centre for Infection Research)

  • Anne-Sophie Gribling-Burrer

    (Helmholtz Centre for Infection Research
    UPR 9002)

  • Redmond P. Smyth

    (Helmholtz Centre for Infection Research
    UPR 9002
    University of Würzburg)

  • Max Kleist

    (Robert Koch Institute
    Freie Universität Berlin)

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.

Suggested Citation

  • Wiep Toorn & Patrick Bohn & Wang Liu-Wei & Marco Olguin-Nava & Anne-Sophie Gribling-Burrer & Redmond P. Smyth & Max Kleist, 2025. "Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59102-9
    DOI: 10.1038/s41467-025-59102-9
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-59102-9
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-59102-9?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Jiaxu Wang & Lin Yang & Anthony Cheng & Cheng-Yong Tham & Wenting Tan & Jefferson Darmawan & Paola Florez Sessions & Yue Wan, 2024. "Direct RNA sequencing coupled with adaptive sampling enriches RNAs of interest in the transcriptome," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.

      More about this item

      Statistics

      Access and download statistics

      Corrections

      All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59102-9. See general information about how to correct material in RePEc.

      If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

      If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

      If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

      For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

      Please note that corrections may take a couple of weeks to filter through the various RePEc services.

      IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.