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nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.

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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.

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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.