RiboSeq.Org: an integrated suite of resources for ribosome profiling data analysis and visualization

Abstract

Ribosome profiling (Ribo-Seq) has revolutionised our understanding of translation, but the increasing complexity and volume of Ribo-Seq data present challenges for its reuse. Here, we formally introduce RiboSeq.Org, an integrated suite of resources designed to facilitate Ribo-Seq data analysis and visualisation within a web browser. RiboSeq.Org comprises several interconnected tools: GWIPS-viz for genome-wide visualisation, Trips-Viz for transcriptome-centric analysis, RiboGalaxy for data processing and the newly developed RiboSeq data portal (RDP) for centralised dataset identification and access. The RDP currently hosts preprocessed datasets corresponding to 14840 sequence libraries (samples) from 969 studies across 96 species, in various file formats along with standardised metadata. RiboSeq.Org addresses key challenges in Ribo-Seq data reuse through standardised sample preprocessing, semi-automated metadata curation and programmatic information access via a REST API and command-line utilities. RiboSeq.Org enhances the accessibility and utility of public Ribo-Seq data, enabling researchers to gain new insights into translational regulation and protein synthesis across diverse organisms and conditions. By providing these integrated, user-friendly resources, RiboSeq.Org aims to lower the barrier to reproducible research in the field of translatomics and promote more efficient utilisation of the wealth of available Ribo-Seq data.