SARS-CoV-2 Data Analysis and Monitoring with Galaxy

training COVID-19

From 2021-08-09 to 2021-08-12 - Add to your Calendar

The goal of this workshop is to build capacity in SARS-CoV-2 data analysis and data management, including data submission to ENA. After the workshop, all participants will be able to upload viral sequencing data, call all variants, create a variety of reports and create consensus alignments.

It will be a 4-day event introducing scalable and reproducible SARS-CoV-2 data analysis with Galaxy. The sessions will be pre-recorded and provided in advance. During the workshop, there will be live support in chat and live Q&A sessions, in which experts will answer questions.

  • WHEN: August 9-12, 2021
  • WHO: Open for everybody, but the target audience is clinicians and researchers that deal with SARS-CoV-2 sequencing data.
  • COST: Free.
  • FORMAT: Virtual and asynchronous. All training sessions will be pre-recorded and provided in advance.
  • SUPPORT:
    • Live support in chat (Slack Channel), in which experts will answer questions on a peer-to-peer basis.
    • Real-Time Q&A sessions on days 3 and 4 (9 am and 4 pm CEST).
  • INFRASTRUCTURE: European Galaxy server and the Galaxy Training Material. Both will stay accessible and open after the training.
  • Contact us if you have questions.

sars-cov-2-workshop


Register now


Program

Some material is still in preparation (WIP)

Day 1 (9.8.2021) - Introduction to Galaxy

Topic Speaker Material Duration
A very short introduction to Galaxy Anton Nekrutenko WIP / WIP Lecture  
Galaxy 101   WIP / WIP Hands-on tutorial
WIP History
 
Demo Anton Nekrutenko WIP / WIP Lecture  
  Anton Nekrutenko WIP / WIP Hands-on tutorial
WIP History
 

Day 2 (10.8.2021) - Data Upload & Quality Control

Topic Speaker Material Duration
Real-Time Q&A session (9 am CEST) All experts   1h
Quality control of reads Florian Heyl / Lecture 40m
  Florian Heyl / Hands-on tutorial
WIP History
1h 10m
Mapping of reads Peter van Heusden / Lecture 10m
  Peter van Heusden / Hands-on tutorial
WIP History
20m
Using dataset collections Anton Nekrutenko WIP / WIP Lecture  
  Anton Nekrutenko / WIP Hands-on tutorial
WIP History
 
Data cleaning workflow   WIP / WIP Lecture  
    WIP / WIP Hands-on tutoria
WIP History
 
Real-Time Q&A session (4 pm CEST) All experts   1h

Day 3 (11.8.2021) - SARS-CoV-2 Data Analysis on Public Datasets

Topic Speaker Material Duration
Real-Time Q&A session (9 am CEST) All experts   1h
Variant calling, reporting, consensus building (with Galaxy GUI)   WIP / WIP Lecture  
    / WIP Hands-on tutorial
WIP History
 
Variant calling, reporting, consensus building (with Galaxy CLI) Simon Bray WIP / WIP Lecture  
  Simon Bray / WIP Hands-on tutorial
WIP History
 
Real-Time Q&A session (4pm CEST) All experts   1h

Both sessions will be in parallel. The first session is intended for wet-lab scientists and the second for people more familiar with a CLI.

Day 4 (12.8.2021) - Visualisation & Data Export

Topic Speaker Material Duration
Real-Time Q&A session (9 am CEST) All experts   1h
Upload data to ENA   WIP / Lecture  
    WIP / WIP Hands-on tutorial
WIP History
 
Upload data to a local datastore   WIP / WIP Lecture  
    WIP / WIP Hands-on tutorial
WIP History
 
Introduction to viral Beacon   WIP / WIP Lecture  
    WIP / WIP Hands-on tutorial  
Using and Customising ObservableHQ   WIP / WIP Lecture  
    WIP / WIP Hands-on tutorial  
Real-Time Q&A session (4 pm CEST) All experts   1h

Logistics

Content delivery

This is a global workshop delivered asynchronously. In practice, this means that you will have training materials available to explore them at your own pace, without any time constraints:

  • Lectures: pre-recorded videos with the theoretical explanation of the lesson.
  • Hands-on: a step-by-step explanation of the tutorials.
  • Histories: Galaxy history with all that you need to reproduce what is shown in the hands-on part.
  • Tutorials: it includes all the required information to perform the data analysis.

Most of these are available already, and they will all stay available after the workshop. All the recordings have manually-curated captions in English.

Communication channels

Should you have any questions, the instructors will be available in chat. We will use the Slack space of the Galaxy Training Network. Depending on your location you might need to use a VPN, so please make sure that you can join Slack before the workshop.

During the week of the workshop, the instructors will be there to reply to your questions. Please be aware of the time zones, the instructors are scattered all over the world and sometimes you may have to be patient to get a reply.

Technical requirements

You don’t need a specific operating system or software installed, all you need is a browser and internet connection.

To do the hands-on on your own, you will need a Galaxy account. Please register at https://usegalaxy.eu.

You will receive an email to confirm your account before you can start using Galaxy.

Certificates

If you need a certificate, you can request it at the end of the workshop. Please make sure to keep all the work over the 4 days, stay active in the discussions and fill out the final survey that we will send around.

Code of Conduct

Everyone is expected to abide by the Code of Conduct (CoC) to make this environment welcoming and friendly for everyone.

Instructors & helpers

Name Location
Björn Grüning Germany
Wolgang Maier Germany
Anton Nekrutenko USA
Peter van Heusden South Africa
Simon Bray Germany
Erik Hjerde Norway
Annbjørg Barbakken Norway
Kjell Petersen Norway
Steven Morgan Australia
Gareth Price Australia
Anna Syme Australia
Igor Makunin Australia
Valentine Murigneux Australia
Michael Thang Australia