Sustainable software solutions for two widely used tools in genomic research

基因组学研究是医学、育种和应用进化研究的基础。最近的技术进步现在允许整个基因组序列的具有成本效益的重建。这极大地推动了基因组学研究，因为现在我们可以第一次研究大量全基因组组装体之间的基因组和基因组差异。然而，用于基因组比较的计算工具仍处于起步阶段。我们已经开发了两个广泛使用的软件工具，plotsi和plotsr，以识别和可视化基因组序列之间的结构差异。这两种工具都遵循一种独特的方法，即它们实际上不是从搜索基因组学差异开始，而是首先识别所有共线区域。根据定义，所有其他区域都是重排，可以很容易地识别并提供最准确的结果。在这个项目中，我们将开发资源，以确保这些工具的可持续使用，并为进一步开发创建框架。具体来说，我们建议开发新的文档，根据当前标准重构源代码，创建最佳实践指南，自动化源代码检查和质量测试，以实现软件存储库的长期稳定性，同时允许社区开发人员更新软件。最后，我们还将为在公共分析服务器（如Galaxy Europe）上使用plotsr和plotsi生成工作流。我们相信，这个项目将使更大的科学界更容易使用plotsr和plotsi，并确保它们得到持续的维护和进一步的发展。

Genomics research is fundamental in medical, breeding, and applied evolutionary studies. Recent technological advances now allow cost-efficient reconstruction of the entire genomic sequence. This has given a significant boost to genomics research as now we can study the genomes and genomic differences between a multitude of whole-genome assemblies for the first time. However, computational tools for genome comparison are still in their infancy. We have developed two widely used software tools, syri and plotsr, to identify and visualise structural differences between genomic sequences. Both tools follow a unique approach where they actually do not start by searching for genomics differences, but instead identify all colinear regions first. By definition, all other regions are rearrangements, which can be identified easily and provide the most accurate results. In this project, we will develop resources to ensure sustainable usage of these tools and create frameworks for further development. Specifically we propose to develop new documentation, to refactor the source code to the current standards, to create best-practices guidelines, to automate source code-checking and quality testing to achieve long-term stability of the software repositories while allowing community developers to update the software. Finally, we will also generate workflows for the use of syri and plotsr on public analysis servers like Galaxy Europe. We believe this project will make both syri and plotsr more accessible to the larger scientific community as well as ensure that they are continuously maintained and further developed.