2nd Galaxy-ELIXIR webinar series: Open Data Infrastructures to tackle COVID-19 pandemic

Wed 20 January 2021 to Wed 24 February 2021

Galaxy project logoThe Galaxy Community and ELIXIR organise a second webinar series to demonstrate how open software and public research infrastructures can be used in analysing and publishing SARS-CoV2 data.

In a series of six webinar sessions, experts from ELIXIR and the global Galaxy community from the US, Australia and Europe will demonstrate how open access and open science are fundamental for fast and efficient response to public health crises. The series follows on the first Galaxy-ELIXIR webinar series organised in April-May 2020. It will introduce the latest Galaxy tools developed for working with SARS-CoV-2 data and discuss some of the challenges in accessing, analysing and interpreting them.

More information about Galaxy analyses of COVID-19 data: covid19.galaxyproject.org
To get involved: galaxyproject.org/community
Training materials: training.galaxyproject.org
Further information: usegalaxy.org

Programme (now completed)

Session 1: COVID-19 analysis in Galaxy: Lessons learned and introduction to the series

20 January 2021, 17.00-18.00 CET (starts at 16.00 GMT, 11.00 EST, 8.00 PST)

The first session summarised the developments in Galaxy over the past eight months and introduced the latest tools for COVID-19 related research:

  • WorkflowHub, Dockstore
  • Single-tool view, simplified workflow run-form
  • Scaling and performance improvements over the last 9 month
  • Paper-Cut event(s)
  • Galaxy plans for the next years


  • Anton Nekrutenko
  • Marius van den Beek

Slide deck 

Session 2: Importance of (open) infrastructures in responding to a pandemic

27 January 2021, 17.00-18.00 CET (starts at 16.00 GMT, 11.00 EST, 8.00 PST)

The second session presents some of the data resources used to deposit and access SARS-CoV2 data. It also covered the critical importance of open access data to respond to epidemic outbreaks efficiently.

  • Data resources
  • Analysis resources
  • Interoperability


  • Andrew Lonie
  • Guy Cochrane
  • Björn Grüning
  • Frederik Coppens
  • Nadim Rahman

Slide deck 

Session 3: Supporting the COVID-19 Data portal: viral data cleaning from human reads and submission to ENA

3 February 2021, 17.00-18.00 CET (starts at 16.00 GMT, 11.00 EST, 8.00 PST)

This session presents the COVID-19 Data Portal and the tools to clean and submit data to open access repositories:

  • Submission tool to European Nucleotide Archive
  • Data preprocessing and cleaning


  • Ignacio Eguinoa
  • Bert Droesbeke
  • Frederik Coppens
  • Miguel Roncoroni

Slide deck 

Session 4: Insights from selection analysis of complete genomes and read-level data

10 February 2021, 17.00-18.00 CET (starts at 16.00 GMT, 11.00 EST, 8.00 PST)


  • Sergei Pond

Slide deck not yet available 

Session 5: Viral Beacon and Galaxy variant workflows

17 February 2021 | 17.00–18.00 CET (starts at 16.00 GMT, 11.00 EST, 8.00 PST)


  • Bjoern Gruening
  • Babita Singh
  • Wolfgang Maier

Variant Workflows Slide deck 

Viral Beacons Slide deck 

Session 6: DRS, long-read-sequencing, proteomics and more — an update to recent COVID-19 workflow developments

24 February 2021, 17.00-18.00 CET (starts at 16.00 GMT, 11.00 EST, 8.00 PST)


  • Milad Miladi
  • Nathan Roach
  • Pratik Jagtap
  • Subina Mehta

Slide deck 



The analyses have been performed using the Galaxy platform and open source tools from BioConda. Tools were run using XSEDE resources maintained by the Texas Advanced Computing Center (TACC ), Pittsburgh Supercomputing Center (PSC), and Indiana University in the U.S., de.NBIVSC cloud resources and  IFB cluster resources on the European side, STFC-IRIS at the Diamond Light Source, and ARDC cloud resources in Australia.

Galaxy Project    European Galaxy Project    Australian Galaxy Project    bioconda   XSEDE    TACC    de.NBI   ELIXIR   PSC   Indiana University    Galaxy Training Network    Bio Platforms Australia    Australian Research Data Commons     VIB   ELIXIR Belgium    Vlaams Supercomputer Center  EOSC-Life   Datamonkey  IFB

See also: Galaxy Community