riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow

Cope AL, Anderson F, Favate JS, Jackson M, Mok A, Kurowska A, MacKenzie E, Shivakumar V, Tilton P, Winterbourne SM, Xue S, Kavoussanakis K, Lareau LF, Shah P, Wallace EWJ. 2022. Bioinformatics 38(8): 2358-2360
DOI
https://doi.org/10.1093/bioinformatics/btac093

Abstract

Motivation

Ribosome profiling, or Ribo-seq, is the state-of-the-art method for quantifying protein synthesis in living cells. Computational analysis of Ribo-seq data remains challenging due to the complexity of the procedure, as well as variations introduced for specific organisms or specialized analyses.

Results

We present riboviz 2, an updated riboviz package, for the comprehensive transcript-centric analysis and visualization of Ribo-seq data. riboviz 2 includes an analysis workflow built on the Nextflow workflow management system for end-to-end processing of Ribo-seq data. riboviz 2 has been extensively tested on diverse species and library preparation strategies, including multiplexed samples. riboviz 2 is flexible and uses open, documented file formats, allowing users to integrate new analyses with the pipeline.

Availability and implementation

riboviz 2 is freely available at github.com/riboviz/riboviz.