riboviz 2：一个灵活且强大的核糖体谱数据分析和可视化工作流程。

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

机构信息

Department of Genetics, Rutgers University, Piscataway, NJ 08854-8082, USA.

Institute for Cell Biology and SynthSys, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK.

出版信息

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

DOI:10.1093/bioinformatics/btac093

PMID:35157051

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9004635/

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.

摘要

动机

核糖体分析（ribosome profiling，或 Ribo-seq）是定量研究活细胞中蛋白质合成的最先进方法。由于该方法的复杂性，以及针对特定生物体或专门分析引入的变化，对 Ribo-seq 数据进行计算分析仍然具有挑战性。

结果

我们提出了 riboviz 2，这是一个经过更新的 riboviz 软件包，用于对 Ribo-seq 数据进行全面的基于转录本的分析和可视化。riboviz 2 包括一个基于 Nextflow 工作流管理系统的分析工作流程，用于端到端处理 Ribo-seq 数据。riboviz 2 已经在多种物种和文库制备策略上进行了广泛的测试，包括多重样本。riboviz 2 具有灵活性，并使用开放、有文档记录的文件格式，允许用户将新的分析集成到管道中。