RiboGalaxy：基于 Galaxy 的核糖体分析数据处理网络平台 - 2023 年更新。

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

机构信息

School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland; SFI Centre for Research Training in Genomics Data Science, University College Cork, Cork, Ireland.

EIRNA Bio Ltd, Bioinnovation Hub, College Rd, Cork, T12 TP07, Ireland.

出版信息

J Mol Biol. 2023 Jul 15;435(14):168043. doi: 10.1016/j.jmb.2023.168043. Epub 2023 Mar 9.

DOI:10.1016/j.jmb.2023.168043

PMID:37356899

Abstract

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.

摘要

核糖体图谱（Ribo-Seq）以亚密码子分辨率捕获细胞中整个转录组中核糖体位置的“快照”，提供对基因表达的深入了解，并能够发现新的翻译区域。基于 Galaxy 的 Ribo-Seq 数据处理平台 RiboGalaxy（https://ribogalaxy.genomicsdatascience.ie/）是 RiboSeq.Org（https://riboseq.org/）的资源。RiboSeq.Org 是一个在线门户，提供了一组用于处理和分析 Ribo-Seq 数据的集成工具。在这次 RiboGalaxy 更新中，我们对 RiboGalaxy 上提供的工具以及后端资源的管理方式进行了更改。例如，为了提高 Riboseq.Org 资源之间的互操作性，我们添加了一些工具，将 RiboGalaxy 的输出与 Trips-Viz 和 GWIPS-viz 浏览器链接起来，用于下游分析和可视化。RiboGalaxy 的后端现在利用 Ansible 配置管理，提高了其稳定性，作业在 Singularity 容器中执行，并由 Slurm 管理，分别提高了可重复性和性能。