G2GSnake：一种用于宿主-病原体基因组关联研究的Snakemake工作流程。

G2GSnake: a Snakemake workflow for host-pathogen genomic association studies.

作者信息

Xu Zhi Ming, Naret Olivier, Oumelloul Mariam Ait, Fellay Jacques

机构信息

School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland.

Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.

出版信息

Bioinform Adv. 2023 Oct 4;3(1):vbad142. doi: 10.1093/bioadv/vbad142. eCollection 2023.

DOI:10.1093/bioadv/vbad142

PMID:37840906

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10576169/

Abstract

SUMMARY

Joint analyses of paired host and pathogen genome sequences have the potential to enhance our understanding of host-pathogen interactions. A systematic approach to conduct such a joint analysis is through a "genome-to-genome" (G2G) association study, which involves testing for associations between all host and pathogen genetic variants. Significant associations reveal host genetic factors that might drive pathogen variation, highlighting biological mechanisms likely to be involved in host control and pathogen escape. Here, we present a Snakemake workflow that allows researchers to conduct G2G studies in a reproducible and scalable manner. In addition, we have developed an intuitive R Shiny application that generates custom summaries of the results, enabling users to derive relevant insights.

AVAILABILITY AND IMPLEMENTATION

G2GSnake is freely available at: https://github.com/zmx21/G2GSnake under the MIT license.

摘要

对配对的宿主和病原体基因组序列进行联合分析，有可能增进我们对宿主-病原体相互作用的理解。进行这种联合分析的一种系统方法是通过“基因组对基因组”（G2G）关联研究，该研究涉及测试所有宿主和病原体遗传变异之间的关联性。显著的关联揭示了可能驱动病原体变异的宿主遗传因素，突出了可能参与宿主控制和病原体逃逸的生物学机制。在这里，我们展示了一个Snakemake工作流程，使研究人员能够以可重复和可扩展的方式进行G2G研究。此外，我们还开发了一个直观的R Shiny应用程序，可生成结果的自定义摘要，使用户能够得出相关见解。