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Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data

Author

Listed:
  • Yaqi Su

    (Zhejiang University
    Zhejiang University
    University of California)

  • Zhejian Yu

    (Zhejiang University
    Zhejiang University)

  • Siqian Jin

    (Zhejiang University
    Zhejiang University)

  • Zhipeng Ai

    (Zhejiang University)

  • Ruihong Yuan

    (Zhejiang University)

  • Xinyi Chen

    (Zhejiang University
    Zhejiang University)

  • Ziwei Xue

    (Zhejiang University
    Zhejiang University)

  • Yixin Guo

    (Zhejiang University
    Zhejiang University)

  • Di Chen

    (Zhejiang University
    Zhejiang University)

  • Hongqing Liang

    (Zhejiang University)

  • Zuozhu Liu

    (Zhejiang University)

  • Wanlu Liu

    (Zhejiang University
    Zhejiang University
    Zhejiang University
    Zhejiang University)

Abstract

The advancement of Long-Read Sequencing (LRS) techniques has significantly increased the length of sequencing to several kilobases, thereby facilitating the identification of alternative splicing events and isoform expressions. Recently, numerous computational tools for isoform detection using long-read sequencing data have been developed. Nevertheless, there remains a deficiency in comparative studies that systemically evaluate the performance of these tools, which are implemented with different algorithms, under various simulations that encompass potential influencing factors. In this study, we conducted a benchmark analysis of thirteen methods implemented in nine tools capable of identifying isoform structures from long-read RNA-seq data. We evaluated their performances using simulated data, which represented diverse sequencing platforms generated by an in-house simulator, RNA sequins (sequencing spike-ins) data, as well as experimental data. Our findings demonstrate IsoQuant as a highly effective tool for isoform detection with LRS, with Bambu and StringTie2 also exhibiting strong performance. These results offer valuable guidance for future research on alternative splicing analysis and the ongoing improvement of tools for isoform detection using LRS data.

Suggested Citation

  • Yaqi Su & Zhejian Yu & Siqian Jin & Zhipeng Ai & Ruihong Yuan & Xinyi Chen & Ziwei Xue & Yixin Guo & Di Chen & Hongqing Liang & Zuozhu Liu & Wanlu Liu, 2024. "Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-48117-3
    DOI: 10.1038/s41467-024-48117-3
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    References listed on IDEAS

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    3. Feng Yue & Yong Cheng & Alessandra Breschi & Jeff Vierstra & Weisheng Wu & Tyrone Ryba & Richard Sandstrom & Zhihai Ma & Carrie Davis & Benjamin D. Pope & Yin Shen & Dmitri D. Pervouchine & Sarah Djeb, 2014. "A comparative encyclopedia of DNA elements in the mouse genome," Nature, Nature, vol. 515(7527), pages 355-364, November.
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    Cited by:

    1. Nicholas C. Gervais & Rebecca S. Shapiro, 2024. "Discovering the hidden function in fungal genomes," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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