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<p>To address recent challenges in circular RNA (circRNA) analysis, we present CIRI3, a tool for circRNA detection and quantification in terabyte-scale RNA-sequencing datasets. Using dynamic multithreaded task partitioning and a blocking search strategy for junction reads, CIRI3 is an order of magnitude faster than existing tools, while providing increased accuracy. We identified differentially spliced circRNAs across 2,535 cancer-related samples, and constructed a pretraining model and a biomarker network provided as the CIRIonco database.</p>

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Detecting and quantifying circular RNAs in terabyte-scale RNA-seq datasets with CIRI3

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年10月1日

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  • Xin Zheng,
  • Jinyang Zhang,
  • Lipu Song,
  • Xiang Jennie Li,
  • Fangqing Zhao,
  • Yuan Gao

摘要

To address recent challenges in circular RNA (circRNA) analysis, we present CIRI3, a tool for circRNA detection and quantification in terabyte-scale RNA-sequencing datasets. Using dynamic multithreaded task partitioning and a blocking search strategy for junction reads, CIRI3 is an order of magnitude faster than existing tools, while providing increased accuracy. We identified differentially spliced circRNAs across 2,535 cancer-related samples, and constructed a pretraining model and a biomarker network provided as the CIRIonco database.