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

doi:10.1093/bioinformatics/btac093

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 journal › Article › peer-review

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.

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 language	English
Article number	btac093
Pages (from-to)	2358-2360
Number of pages	4
Journal	Bioinformatics
Volume	38
Issue number	8
Early online date	14 Feb 2022
DOIs	https://doi.org/10.1093/bioinformatics/btac093
Publication status	Published - 15 Apr 2022

Access to Document

10.1093/bioinformatics/btac093Licence: Creative Commons: Attribution (CC-BY)

WallaceEtalB2022Riboviz2AFlexibleAndRobustRibosomeFinal published version, 1.45 MBLicence: Creative Commons: Attribution (CC-BY)

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
Dynamic regulation of mRNA processing in adapting fungi
Wallace, E.
UK-based charities
19/01/18 → 18/01/23
Project: Research

Cite this

Cope, A. L., Anderson, F., Favate, J., Jackson, M., Mok, A., Kurowska, A., Liu, J., MacKenzie, E., Shivakumar, V., Tilton, P., Winterbourne, S., Xue, S., Kavoussanakis, K., Lareau, L. F., Shah, P., & Wallace, E. W. J. (2022). riboviz 2: A flexible and robust ribosome profiling data analysis and visualization workflow. Bioinformatics, 38(8), 2358-2360. [btac093]. https://doi.org/10.1093/bioinformatics/btac093

@article{3eb45cc93a674b759ceb2f82ef31ddf0,

title = "riboviz 2: A flexible and robust ribosome profiling data analysis and visualization workflow",

abstract = "MotivationRibosome 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.ResultsWe 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.Availabilityriboviz 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 Junchen Liu 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.}",

year = "2022",

month = apr,

day = "15",

doi = "10.1093/bioinformatics/btac093",

language = "English",

volume = "38",

pages = "2358--2360",

journal = "Bioinformatics",

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publisher = "Oxford University Press",

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Cope, AL, Anderson, F, Favate, J, Jackson, M, Mok, A, Kurowska, A, Liu, J, MacKenzie, E, Shivakumar, V, Tilton, P, Winterbourne, S, Xue, S, Kavoussanakis, K, Lareau, LF, Shah, P & Wallace, EWJ 2022, 'riboviz 2: A flexible and robust ribosome profiling data analysis and visualization workflow', Bioinformatics, vol. 38, no. 8, btac093, pp. 2358-2360. https://doi.org/10.1093/bioinformatics/btac093

TY - JOUR

T1 - riboviz 2

T2 - A flexible and robust ribosome profiling data analysis and visualization workflow

AU - Cope, Alexander L

AU - Anderson, Felicity

AU - Favate, John

AU - Jackson, Michael

AU - Mok, Amanda

AU - Kurowska,, Anna

AU - Liu, Junchen

AU - MacKenzie, Emma

AU - Shivakumar, Vikram

AU - Tilton, Peter

AU - Winterbourne, Sophie

AU - Xue, Siyin

AU - Kavoussanakis, Kostas

AU - Lareau, Liana F

AU - Shah, Premal

AU - Wallace, Edward W. J.

PY - 2022/4/15

Y1 - 2022/4/15

N2 - MotivationRibosome 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.ResultsWe 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.Availabilityriboviz 2 is freely available at github.com/riboviz/riboviz.

AB - MotivationRibosome 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.ResultsWe 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.Availabilityriboviz 2 is freely available at github.com/riboviz/riboviz.

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DO - 10.1093/bioinformatics/btac093

M3 - Article

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SN - 1367-4803

VL - 38

SP - 2358

EP - 2360

JO - Bioinformatics

JF - Bioinformatics

IS - 8

M1 - btac093

ER -

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

Abstract / Description of output

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Projects

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

Dynamic regulation of mRNA processing in adapting fungi

Cite this