SARS-CoV-2 Data Analysis and Monitoring with Galaxytraining 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.
- 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.
Some material is still in preparation (WIP)
Day 1 (9.8.2021) - Introduction to Galaxy
|A very short introduction to Galaxy||Anton Nekrutenko||WIP / WIP Lecture|
|Galaxy 101||WIP / WIP Hands-on tutorial
|Demo||Anton Nekrutenko||WIP / WIP Lecture|
|Anton Nekrutenko||WIP / WIP Hands-on tutorial
Day 2 (10.8.2021) - Data Upload & Quality Control
Day 3 (11.8.2021) - SARS-CoV-2 Data Analysis on Public Datasets
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
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.
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.
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.
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
|Peter van Heusden||South Africa|