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Updated: Aug 5, 2026
08:25
Identification of Circular RNAs using RNA Sequencing
Published on: November 14, 2019
Efficient reconstruction of full-length RNA isoforms using ISAtools and large-scale PacBio circular consensus
Hu Chen1,2, Yu-Chen Zhang1, Qi Dai1
1College of Life Science and Medicine, Zhejiang Sci-Tech University, Second Street 928, Qiantang District, Hangzhou 310018, China.
Briefings in Bioinformatics
|July 30, 2026
Summary
ISAtools is a new framework for analyzing long-read RNA sequencing data. It accurately reconstructs and quantifies RNA isoforms from PacBio CCS data, improving transcript discovery and analysis efficiency.
Area of Science:
- Genomics
- Transcriptomics
- Bioinformatics
Background:
- Accurate reconstruction and quantification of full-length RNA isoforms are challenging in long-read RNA sequencing due to artifacts and complex splicing.
- Existing scalable and annotation-flexible analysis frameworks for PacBio CCS data are limited.
Purpose of the Study:
- To present ISAtools, an efficient framework designed for PacBio CCS data.
- To enable scalable and annotation-flexible analysis of long-read RNA sequencing data.
Main Methods:
- Developed a splice site chain representation for unified read alignment and transcript annotation.
- Integrated unsupervised density-based clustering for transcription start and end site detection.
- Implemented a truncation-aware quantification strategy.
Main Results:
- ISAtools accurately reconstructs annotated and novel isoforms with reliable splice structures and transcript boundaries.
- Demonstrated high computational efficiency, processing up to 80 million reads in ~21 minutes.
- Showcased scalability to nearly 1 billion reads in under 4 hours with ~8 GB memory.
Conclusions:
- ISAtools provides an efficient and accurate framework for PacBio CCS data analysis.
- The framework supports large-scale Iso-Seq studies, enhancing RNA isoform reconstruction and quantification.
- ISAtools addresses limitations in current analysis frameworks for long-read RNA sequencing.
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