RiboPy

Binary storage and analysis framework for ribosome profiling data

RiboPy stores and analyzes ribosome profiling (Ribo-seq) data using a binary “ribo” file format that organizes ribosome occupancy by footprint length. It integrates with the RiboFlow pipeline to process raw ribosomal profiling sequencing data and enables downstream analysis in R and Python.

Key Features:

• Ribo Binary File Format: Stores ribosome occupancy data grouped by specific ribosome footprint lengths to preserve read-length information and optimize large-scale data handling.
• RiboFlow Processing Pipeline: Converts raw ribosome profiling sequencing reads into ribo files with built-in parallelization for scalable computation.
• R and Python Interfaces: Provides RiboR and RiboPy interfaces for accessing ribosome profiling quality control metrics, generating plots, and performing downstream analyses.
• End-to-End Workflow Support: Supports processing from raw sequencing data to footprint-length-resolved translational analyses.

Scientific Applications:

• Translation Dynamics and Protein Synthesis Studies: Enables footprint-length-specific quantification of ribosome occupancy to investigate translation mechanisms and estimate protein abundance.

Methodology:

RiboFlow processes raw ribosome profiling sequencing data into ribo binary files, organizing reads by footprint length. RiboPy and RiboR access these structured datasets to compute quality metrics, generate visualizations, and perform length-resolved analyses of ribosome occupancy.