Viral pathogen data analysis with Galaxy

The success of the GalaxyProject SARS-CoV-2 analysis effort during the COVID-19 pandemic has boosted interest in Galaxy as a platform for viral pathogen data analysis. Our ensuing involvement in international projects and collaborations with partners from virology labs from around the world, has given us the opportunity to keep developing Galaxy tools, workflows, complete analysis solutions and learning resources for a diverse set of very real-world viral pathogen data analysis needs. These slides of a talk at GCC 2024 provide an overview of our efforts of the last three years: on the SARS-CoV-2 side of things, we have, within the BY-COVID project, built an integrated analysis system for surveillance based on viral sequencing data around initial workflows for analysis of such data. We have also created training resources around analysis and handling of SARS-CoV-2 sequencing data and used, and are using, this material, the workflows and the analysis system in various training events. The Galaxy integration of pangolin, one of the most widely tools for SARS-CoV-2 lineage assignment, has been developed to an extent that it serves as an example of what a Galaxy tool integration can offer in terms of ease of use, scalability and reproducibility. Regarding other viral pathogens, we have recently developed sequencing data analysis workflows (similar to the ones for SARS-CoV-2) for Lumpy skin disease virus and for Avian influenza virus. These developments happened in close collaboration with international experts for the respective viruses and have already been evaluated on real-world data as part of several workshops for members of veterinarian diagnostic laboratories. For AIV, current work revolves around scaling the throughput of the workflow to what's already possible for SARS-CoV-2. As a tool useful for many viral pathogens, we recently integrated varVAMP into Galaxy. This novel primer design tool lets you generate entire tiled-amplicon primer schemes even for viral clades with significant diversity. As auxiliary data for tools and workflows, public Galaxy instances are also hosting existing primer schemes and collections of published reference data (of particular importance for influenza virus genome analysis). For simplified access to all of these resources, we are currently finalizing virology.usegalaxy.eu, a subdomain of Galaxy Europe, which can serve as a landing page for everyone interested in doing virology-related bioinformatics with the Galaxy platform. Links to resources mentioned on the slides: https://www.infectious-diseases-toolkit.org/showcase/covid19-galaxy the IDTk showcase developed within BY-COVID with links to all other SARS-CoV-2-related resources https://virology.usegalax.eu new subdomain of Galaxy Europe (under development) from which all workflows and resources for all viral pathogens will be easy to discover Links to training resources: https://gxy.io/GTN:T00316 https://gxy.io/GTN:T00236 https://gxy.io/GTN:T00347 https://gxy.io/GTN:T00308 https://gxy.io/GTN:T00437 https://gxy.io/GTN:S00064 https://gxy.io/GTN:T00159