RiboGalaxy: A Galaxy-based Web Platform for Ribosome Profiling Data Processing – 2023 Update

[Display omitted] •Ribo-Seq enables gene expression assessment at the transcriptional and translational level.•RiboGalaxy is a Galaxy-based platform for processing Ribo-Seq from reads to alignments.•RiboGalaxy links raw Ribo-Seq data with Trips-Viz and GWIPS-viz visualisation.•RiboGalaxy is availabl...

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Bibliographic Details
Published in:Journal of molecular biology 2023-07, Vol.435 (14), p.168043-168043, Article 168043
Main Authors: Fedorova, Alla D., Tierney, Jack A.S., Michel, Audrey M., Baranov, Pavel V.
Format: Article
Language:English
Subjects:
galaxy
Internet
mRNA translation
Protein Biosynthesis
Reproducibility of Results
ribo-Seq
ribosome profiling
Ribosome Profiling - methods
Ribosomes - genetics
Ribosomes - metabolism
RNA, Messenger - genetics
Software
translatome
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Summary:[Display omitted] •Ribo-Seq enables gene expression assessment at the transcriptional and translational level.•RiboGalaxy is a Galaxy-based platform for processing Ribo-Seq from reads to alignments.•RiboGalaxy links raw Ribo-Seq data with Trips-Viz and GWIPS-viz visualisation.•RiboGalaxy is available at a new address: https://ribogalaxy.genomicsdatascience.ie/. Ribosome profiling (Ribo-Seq) captures a “snapshot” of ribosomes’ locations at the entire transcriptome of a cell at sub-codon resolution providing insights into gene expression and enabling the discovery of novel translated regions. RiboGalaxy (https://ribogalaxy.genomicsdatascience.ie/), a Galaxy-based platform for processing Ribo-Seq data is a RiboSeq.Org (https://riboseq.org/) resource. RiboSeq.Org is an online gateway to a set of integrated tools for the processing and analysis of Ribo-Seq data. In this RiboGalaxy update we introduce changes to both the tools available on RiboGalaxy and to how the resource is managed on the backend. For example, in order to improve interoperability between Riboseq.Org resources, we added tools that link RiboGalaxy outputs with Trips-Viz and GWIPS-viz browsers for downstream analysis and visualisation. RiboGalaxy’s backend now utilises Ansible configuration management which enhances its stability and jobs are executed within Singularity containers and are managed by Slurm, strengthening reproducibility and performance respectively.
ISSN:0022-2836
1089-8638
DOI:10.1016/j.jmb.2023.168043