Viral pathogen data analysis with Galaxy
Creators: name: Maier, Wolfgang
name: Van Heusden, Peter
name: Rasche, Helena
name: Nekrutenko, Anton
Publisher: name: F1000 Research Limited
Year: 2024

description: The success of the GalaxyProject SARS-CoV-2 analysis effort during the COVID-19 pandemic has boosted<br>
interest in Galaxy as a platform for viral pathogen data analysis.<br>
Our ensuing involvement in international projects and collaborations with partners from virology labs<br>
from around the world, has given us the opportunity to keep developing Galaxy tools, workflows,<br>
complete analysis solutions and learning resources for a diverse set of very real-world viral pathogen<br>
data analysis needs.<br>
<br>
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.<br>
 <br>
 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.<br>
 <br>
 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.<br>
  
 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.<br>
 <br>
 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.<br>
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 For AIV, current work revolves around scaling the throughput of the workflow to what's already possible for SARS-CoV-2.<br>
  
 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.<br>
  
 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).

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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.<br>
<br>
<br>
<b>Links to resources mentioned on the slides:</b>


 https://www.infectious-diseases-toolkit.org/showcase/covid19-galaxy<br>
 <br>
 the IDTk showcase developed within BY-COVID with links to all other SARS-CoV-2-related resources<br>
  
 https://virology.usegalax.eu<br>
 <br>
 new subdomain of Galaxy Europe (under development) from which all workflows and resources for all viral pathogens will be easy to discover

<br>
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