RiboDoc: A Docker-based package for ribosome profiling analysis

Computational and Structural Biotechnology Journal

Olivier Namy¹  Agnès Baudin-Baillieu²  Hugo Arbes²  Stéphane Demais²  Pauline François² 

[1]Corresponding author.

[2]Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France

关键词: Riboseq;    Bioinformatics;    FAIR;    Translation;    Ribosome;    Docker;   

DOI  :  

来源: DOAJ

【 摘 要 】

Ribosome profiling (RiboSeq) has emerged as a powerful technique for studying the genome-wide regulation of translation in various cells. Several steps in the biological protocol have been improved, but the bioinformatics part of RiboSeq suffers from a lack of standardization, preventing the straightforward and complete reproduction of published results. Too many published studies provide insufficient detail about the bioinformatics pipeline used. The broad range of questions that can be asked with RiboSeq makes it difficult to use a single bioinformatics tool. Indeed, many scripts have been published for addressing diverse questions. Here (https://github.com/equipeGST/RiboDoc), we propose a unique tool (for use with multiple operating systems, OS) to standardize the general steps that must be performed systematically in RiboSeq analysis, together with the statistical analysis and quality control of the sample. The data generated can then be exploited with more specific tools. We hope that this tool will help to standardize bioinformatics analyses pipelines in the field of translation.

【 授权许可】

Unknown