NextLongIso: a comprehensive Nextflow pipeline for multi-dimensional long-read RNA-seq analysis

Area of Science:

• Genomics
• Transcriptomics
• Bioinformatics

Background:

• Long-read RNA sequencing (RNA-seq) technologies like PacBio and ONT offer direct full-length transcript characterization.
• Current analysis of long-read RNA-seq data is fragmented across multiple tools, hindering a unified view of transcriptomic complexity.

Purpose of the Study:

• To present NextLongIso, a scalable and reproducible Nextflow pipeline for coordinated analysis of long-read RNA-seq data.
• To integrate transcript discovery with downstream regulatory analyses for a comprehensive understanding of transcriptomic variation.

Main Methods:

• NextLongIso is implemented in Nextflow, ensuring scalability and reproducibility.
• The pipeline integrates transcript discovery with analyses of alternative splicing, isoform switching, transcript boundary dynamics, and transposable element transcription.
• It supports both PacBio and Oxford Nanopore Technologies (ONT) datasets.

Main Results:

• NextLongIso provides a unified framework for analyzing multiple layers of transcript regulation.
• It facilitates joint characterization of alternative splicing, isoform switching, and transcript boundary dynamics.
• The pipeline enables the analysis of transposable element-associated transcription from long-read data.

Conclusions:

• NextLongIso streamlines the analysis of long-read RNA-seq data by eliminating the need for complex cross-tool data harmonization.
• This unified framework facilitates the transition from transcript identification to the functional interpretation of transcriptomic variation.
• It enhances the ability to obtain a comprehensive view of transcript structure, expression, and regulatory variation.