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Viral pathogen data analysis with Galaxy

Wolfgang Maier

Galaxy Europe Team

University of Freiburg, Germany

Peter van Heusden, Helena Rasche, Anton Nekrutenko

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The GalaxyProject SARS-CoV-2 analysis effort during the pandemic

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Galaxy resources for SARS-CoV-2 genomic surveillance

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Galaxy resources for SARS-CoV-2 genomic surveillance

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Galaxy resources for SARS-CoV-2 genomic surveillance

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Galaxy resources for SARS-CoV-2 genomic surveillance

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about 500,000 viral samples analysed on usegalaxy.* instances to date

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Full control over all reference data used:

Reproducibility through pinning of key dependencies:

No need to worry about compute; re-analyse truly large sample collections on your server’s infrastructure.

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Galaxy resources for SARS-CoV-2 genomic surveillance

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Going beyond SARS-CoV-2

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Design your viral primer schemes in Galaxy

(coming soon)

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Reliable and fast whole-genome reconstruction for (Capri)pox viruses

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  • tested on public Lumpy skin disease (LSDV) data generated by Sciensano
  • and on freshly obtained isolates during a workshop in Bangladesh last year

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Fast and robust Avian Influenza subtyping and genome reconstruction

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IAEA Regional Training Course on next-generation sequencing and analysis of AIV samples

  • tested on AIV samples obtained by Sciensano in Belgium

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  • and on freshly obtained isolates during a workshop in Slovenia in late 2022

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Galaxy for pathogen data analysis

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Providing viral reference data along with tools and workflows

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Popular tiled amplicon schemes at different versions + the Wuhan-Hu-1

reference genome to get you started with SARS-CoV-2 sequencing data analysis

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Reference sequences capturing the diversity of Influenza A across different gene segments for rapid subtyping with VAPOR

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Bringing it all together

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virology.usegalaxy.eu

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virology.usegalaxy.eu

Public Health SIG at

https://galaxyproject.org/community/

https://training.galaxyproject.org/

training-material/topics/one-health/

Thanks to:

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Marius van den Beek

Dannon Baker

Brad Langhorst

Stephen Shank

​

Steven van Borm

Tomas Klingström

Sergei Pond

Jonas Fuchs

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virology.usegalaxy.eu

Public Health SIG at

https://galaxyproject.org/community/

Thanks to:

​

Marius van den Beek

Dannon Baker

Brad Langhorst

Stephen Shank

​

Steven van Borm

Tomas Klingström

Sergei Pond

Jonas Fuchs

https://training.galaxyproject.org/

training-material/topics/one-health/

watch out for BY-COVID track of the Galaxy Training Academy 2024

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fin