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,; Emma MacKenzie; Vikram Shivakumar; Peter Tilton; Sophie Winterbourne; Siyin Xue; Kostas Kavoussanakis; Liana F Lareau; Premal Shah; Edward W. J.  Wallace

doi:10.1101/2021.05.14.443910

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,, Emma MacKenzie, Vikram Shivakumar, Peter Tilton, Sophie Winterbourne, Siyin Xue, Kostas Kavoussanakis, Liana F Lareau, Premal Shah, Edward W. J. Wallace

Research output: Working paper › Preprint

Abstract / Description of output

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. Many bioinformatic pipelines have been developed, but these pipelines have key limitations in terms of functionality or usability.

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, combining freely available software with custom code. The package is extensively documented and provides example configuration files for organisms spanning the domains of life. riboviz 2 is distinguished by clear separation of concerns between annotation and analysis: prior to a run, the user chooses a transcriptome in FASTA format, paired with annotation for the CDS locations in GFF3 format. The user is empowered to choose the relevant transcriptome for their biological question, or to run alternative analyses that address distinct questions. riboviz 2 has been extensively tested on various 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 language	English
Publisher	bioRxiv, at Cold Spring Harbor Laboratory
Number of pages	5
DOIs	https://doi.org/10.1101/2021.05.14.443910
Publication status	Published - 17 May 2021

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10.1101/2021.05.14.443910Licence: Creative Commons: Attribution (CC-BY)

1 Finished
1 Active

Dynamic regulation of mRNA processing in adapting fungi
Wallace, E.
UK-based charities
19/01/18 → 18/01/24
Project: Research
BBSRC-NSF/BIO: RiboViz for reliable, reproducible and rigorous quantification of protein synthesis from ribosome profiling data.
Wallace, E.
BBSRC
1/05/19 → 30/04/22
Project: Research

Cite this

Cope, A. L., Anderson, F., Favate, J., Jackson, M., Mok, A., Kurowska, A., MacKenzie, E., Shivakumar, V., Tilton, P., Winterbourne, S., Xue, S., Kavoussanakis, K., Lareau, L. F., Shah, P., & Wallace, E. W. J. (2021). riboviz 2: A flexible and robust ribosome profiling data analysis and visualization workflow. bioRxiv, at Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.05.14.443910

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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. Many bioinformatic pipelines have been developed, but these pipelines have key limitations in terms of functionality or usability.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, combining freely available software with custom code. The package is extensively documented and provides example configuration files for organisms spanning the domains of life. riboviz 2 is distinguished by clear separation of concerns between annotation and analysis: prior to a run, the user chooses a transcriptome in FASTA format, paired with annotation for the CDS locations in GFF3 format. The user is empowered to choose the relevant transcriptome for their biological question, or to run alternative analyses that address distinct questions. riboviz 2 has been extensively tested on various 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.",

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

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

Abstract / Description of output

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Projects

Dynamic regulation of mRNA processing in adapting fungi

BBSRC-NSF/BIO: RiboViz for reliable, reproducible and rigorous quantification of protein synthesis from ribosome profiling data.

Cite this