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. 2022 Apr 12;38(8):2358-2360.
doi: 10.1093/bioinformatics/btac093.

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

Alexander L Cope  1 , Felicity Anderson  2 , John Favate  1 , Michael Jackson  3 , Amanda Mok  4 , Anna Kurowska  2 , Junchen Liu  3 , Emma MacKenzie  2 , Vikram Shivakumar  5 , Peter Tilton  1 , Sophie M Winterbourne  2 , Siyin Xue  2 , Kostas Kavoussanakis  3 , Liana F Lareau  4   5 , Premal Shah  1 , Edward W J Wallace  2
Affiliations

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

Alexander L Cope et al. Bioinformatics. .

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.

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Figures

Fig. 1.
Fig. 1.
riboviz pipeline and data structures. (A) riboviz takes in user-provided sequencing, transcript annotation, and configuration files, processes the datasets and generates two major output—transcriptome-specific BAM file and a ribogrid file. These outputs are used to generate sample-specific analyses and summaries, which can be visualized as both static figures and in an interactive R/Shiny application. (B) Structure of the ribogrid file format. Ribogrid is a complete representation of transcript-specific ribosome-footprint data in an H5 file format. Each row indicates reads of a particular length and each column indicates the position of the 5ʹ-end of a footprint. *Optional
Fig. 2.
Fig. 2.
The riboviz 2 data visualization application is powered by R and Shiny and allows users to view various aspects of their data in an interactive manner in a web browser. Shown is an example visualization using data from Guydosh and Green (2014). This dataset is also part of our example datasets repository (https://github.com/riboviz/example-datasets).
See this image and copyright information in PMC

References

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    1. Di Tommaso P. et al. (2017) Nextflow enables reproducible computational workflows. Nat. Biotechnol., 35, 316–319. - PubMed
    1. Guydosh N.R., Green R. (2014) Dom34 rescues ribosomes in 3 untranslated regions. Cell, 156, 950–962. - PMC - PubMed
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