riboviz 2

Transcript-centric Nextflow pipeline for ribosome profiling analysis

RiboViz 2 analyzes ribosome profiling (Ribo-seq) data using a transcript-centric framework that accepts user-defined transcriptomes in FASTA format with corresponding coding sequence (CDS) annotations in GFF3 format. It implements a reproducible workflow for processing and analyzing translational activity across selected transcript sets.

Key Features:

• Transcript-Centric Input: Processes custom transcriptomes (FASTA) with matched CDS annotations (GFF3) to enable targeted translational analyses.
• Nextflow-Based Workflow: Executes a reproducible analysis pipeline using the Nextflow workflow management system integrating external software and custom code.
• Annotation–Analysis Separation: Decouples transcript annotation from downstream analysis, allowing independent selection of transcriptome resources.
• Library Preparation Compatibility: Supports multiple ribosome profiling library preparation strategies, including multiplexed samples.
• Open File Format Integration: Utilizes standardized, documented file formats to facilitate extension and incorporation of additional analyses.

Scientific Applications:

• Global Translation Profiling: Enables transcriptome-wide analysis of translational activity, identification of actively translated regions, and investigation of organism-specific translation mechanisms.

Methodology:

RiboViz 2 processes ribosome profiling reads within a Nextflow-managed pipeline, aligning data to user-specified transcriptomes and CDS annotations, and performing transcript-level analyses while maintaining separation between annotation resources and computational workflows.