BeYond-COVID

Learn about viral pathogen data analysis with Galaxy. Content here has been developed over the course of the COVID-19 pandemic and to a large part under the umbrella of the BY-COVID project as explained in a recent blog post.

Work through the material at your own pace. If you need support contact us via the Slack Channel #gta_BY-COVID.

Organisers(s) orcid logoWolfgang Maier avatar Wolfgang Maier
Instructor(s) orcid logoAnna Syme avatar Anna Symeorcid logoBjörn Grüning avatar Björn GrüningGareth Price avatar Gareth PriceIgor Makunin avatar Igor MakuninMatee Ullah avatar Matee Ullahorcid logoWolfgang Maier avatar Wolfgang Maier

Need help with these tutorials?

Open Slack support channel for this track: comment   #gta_BY-COVID

Viral genomes sequencing data analysis

Here you find three hands-on tutorials demonstrating sequencing data analysis with Galaxy for three, rather different viral pathogens in increasing order of analysis complexity. Feel free to work through all three of them or just pick the one covering the virus you are most interested in, but consider watching first the introductory video, which explains some of the particularities of each virus and the corresponding analysis challenges.

Lesson Slides Hands-on Recordings

Sequencing spectrum viral genomes

Lecture Video

From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
Avian influenza viral strain analysis from gene segment sequencing data
Pox virus genome analysis from tiled-amplicon sequencing data

SARS-CoV-2 genome surveillance system

Learn about how to scale up your Galaxy-based viral sequencing data analysis to batches of samples and how to automate the processing of such batches for highest sample throughput. Watch the introductory video for an overview of the contents of this section and how the pieces are connected.

Lesson Slides Hands-on Recordings

An automated SARS-CoV-2 genome surveillance system built around Galaxy

Lecture Video; Showcase page mentioned in the video

Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
Automating Galaxy workflows using the command line

The usegalaxy.* SARS-CoV-2 Bot in Action

Demo Video

Upload to ENA

Demo Video