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Clair3-RNA: a deep learning-based small variant caller for long-read RNA sequencing data.

Zhenxian Zheng1, Xian Yu1, Lei Chen1

  • 1School of Computing and Data Science, University of Hong Kong, Hong Kong, China.

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|December 22, 2025
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Summary
This summary is machine-generated.

Clair3-RNA is a novel deep learning tool for long-read RNA sequencing variant calling. It improves accuracy across platforms like PacBio and ONT, enabling better gene expression analysis.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Long-read RNA sequencing (lrRNA-seq) offers insights into full-length isoforms and gene expression.
  • High error rates and transcript complexity challenge variant calling in lrRNA-seq data.
  • Existing variant callers struggle with the unique characteristics of lrRNA-seq data.

Purpose of the Study:

  • To introduce Clair3-RNA, the first deep learning variant caller specifically designed for lrRNA-seq data.
  • To enhance variant calling performance by addressing challenges like uneven coverage and RNA editing.
  • To provide a versatile tool supporting multiple lrRNA-seq platforms.

Main Methods:

  • Development of Clair3-RNA, a deep learning model building on the Clair series.
  • Implementation of optimized techniques: uneven coverage normalization, refined training data, RNA editing site discovery, and haplotype phasing.
  • Validation across PacBio (Iso-Seq, MAS-Seq) and Oxford Nanopore (ONT cDNA, dRNA) sequencing platforms.

Main Results:

  • Achieved high SNP F1-scores: ~91% (ONT dRNA004), ~92% (PacBio >=4x coverage).
  • Performance exceeded ~95% (ONT) and ~96% (PacBio) F1-scores with >=10x coverage.
  • Phased variant calling reached ~97% (ONT) and ~98% (PacBio) accuracy.
  • Demonstrated superior performance over existing callers on GIAB samples and accurate RNA editing site identification.

Conclusions:

  • Clair3-RNA significantly advances variant calling for lrRNA-seq data.
  • The tool offers high accuracy and broad platform compatibility for genomic and transcriptomic analyses.
  • Clair3-RNA is an open-source solution for researchers utilizing lrRNA-seq.