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

Alexander L Cope, Felicity Anderson, John Favate, Michael Jackson, Amanda Mok, Anna Kurowska,, Junchen Liu, Emma MacKenzie, Vikram Shivakumar, Peter Tilton, Sophie Winterbourne, Siyin Xue, Kostas Kavoussanakis, Liana F Lareau, Premal Shah, Edward W. J. Wallace

Research output: Contribution to journalArticlepeer-review

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
riboviz 2 is freely available at github.com/riboviz/riboviz.
Original languageEnglish
Article numberbtac093
Number of pages5
JournalBioinformatics
Early online date14 Feb 2022
DOIs
Publication statusE-pub ahead of print - 14 Feb 2022

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