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Updated: Aug 5, 2025
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing
Sébastien Guizard1, Katarzyna Miedzinska1, Jacqueline Smith1
1The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom.
Bioinformatics (Oxford, England)
|March 24, 2023
Summary
Iso-Seq long-read sequencing simplifies transcript identification. The nf-core/isoseq pipeline automates data processing and genome annotation for full-length transcripts and isoforms.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Iso-Seq RNA long-read sequencing identifies full-length transcripts and isoforms.
- Raw sequencing data require extensive processing for complete genome annotation.
Purpose of the Study:
- Introduce nf-core/isoseq, a pipeline for automated Iso-Seq read processing and genome annotation.
- Provide a user-friendly, dependency-light tool adhering to nf-core guidelines.
Main Methods:
- Developed an automated pipeline for Iso-Seq data processing.
- Integrated genome annotation steps within the pipeline.
- Ensured compatibility across multiple computing platforms.
Main Results:
- The nf-core/isoseq pipeline automates the processing of Iso-Seq RNA sequencing data.
- Facilitates genome annotation for full-length transcripts and isoforms.
- The pipeline is designed with minimal dependencies for broad usability.
Conclusions:
- nf-core/isoseq simplifies and automates Iso-Seq data analysis.
- Enhances the efficiency of full-length transcript and isoform identification.
- The pipeline is readily available and adaptable for various research environments.
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