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PubMed · 41034498

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

Xin Zheng·Jinyang Zhang·Lipu Song·Xiang Jennie Li·Fangqing Zhao·Yuan Gao
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Abstract

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.

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RNA, CircularHumansSequence Analysis, RNARNA-SeqNeoplasmsSoftwareRNAJournal Article

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Xin Zheng, Jinyang Zhang, Lipu Song, Xiang Jennie Li, Fangqing Zhao, Yuan Gao. 2025-10-01. Detecting and quantifying circular RNAs in terabyte-scale RNA-seq datasets with CIRI3.. https://doi.org/10.1038/s41587-025-02835-1

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