Sustainable software solutions for two widely used tools in genomic research

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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.