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Updated: Jun 26, 2025
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
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Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data
Yaqi Su1,2,3, Zhejian Yu1,2, Siqian Jin1,2
1Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China.
Nature Communications
|May 10, 2024
Summary
IsoQuant is a top tool for detecting gene isoforms using Long-Read Sequencing (LRS). This study benchmarks thirteen methods, finding IsoQuant, Bambu, and StringTie2 effective for alternative splicing analysis with LRS data.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Long-Read Sequencing (LRS) advances enable longer sequence reads, improving detection of alternative splicing and isoform expression.
- Numerous computational tools exist for isoform detection from LRS data, but systematic performance evaluations are lacking.
- Understanding tool performance under diverse conditions is crucial for accurate alternative splicing analysis.
Purpose of the Study:
- To conduct a comprehensive benchmark analysis of thirteen isoform detection methods implemented in nine distinct tools for Long-Read RNA sequencing (LRS) data.
- To evaluate tool performance using simulated data from various platforms, RNA sequins (sequencing spike-ins) data, and experimental datasets.
- To identify the most effective computational tools for accurate isoform detection and alternative splicing analysis using LRS.
Main Methods:
- Development of an in-house simulator to generate diverse simulated LRS data reflecting different sequencing platforms.
- Performance evaluation of thirteen isoform detection methods across nine different computational tools.
- Utilized simulated data, RNA sequins (sequencing spike-ins) data, and experimental RNA-seq data for comprehensive benchmarking.
Main Results:
- IsoQuant demonstrated highly effective performance in isoform detection using Long-Read Sequencing data.
- Bambu and StringTie2 also exhibited strong performance among the evaluated tools.
- The study identified significant performance variations among tools, highlighting the importance of method selection for LRS data analysis.
Conclusions:
- IsoQuant is a recommended tool for isoform detection with Long-Read Sequencing.
- Bambu and StringTie2 are also robust options for analyzing alternative splicing with LRS data.
- This benchmark provides essential guidance for researchers in alternative splicing analysis and tool development for LRS.
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