Rp-Bp and the Ribotools box for translatome profiling

Abstract

We present the Ribotools “box” for the analysis of matched ribosome profiling (Ribo-seq) and RNA sequencing data. Ribotools can be used in standalone mode or in combination with Rp-Bp for Ribo-seq quality control, open reading frames discovery, translation efficiency, and differential expression analyses. In this work, we use Ribotools to profile the differentiation of human induced pluripotent stem cells (hiPSCs) into cardiomyocytes to reveal a remarkably coherent transition from plastic, signaling-driven to stable, structurally committed cardiac cells, staged through multiple layers of translational control. Together with complementary proteomics, the resulting dataset provides a rich multi-omics resource for investigating the hiPSC model of cardiac lineage commitment. Additionally, we present a reproducible and extensible pipeline for benchmarking translation efficiency analysis tools. Ribotools and Rp-Bp are available on Bioconda and help to make research accessible and reproducible. Detailed documentation, test datasets, and tutorials are available at https://ribotools.readthedocs.io and https://rp-bp.readthedocs.io.