SARS-CoV-2 Data Analysis and Monitoring with Galaxytraining COVID-19
From 2021-12-01 to 2021-12-01 - Add to your Calendar
The goal of this workshop is to enable groups doing SARS-CoV-2 sequencing using amplicon methods (like ARTICv3, ARTICv4, NEBNext VarSkip, Midnight, …) to learn how to use pre-built workflows to quickly generate consensus sequences. After the workshop, participants will be able to upload viral sequencing data from Illumina and ONT sequencers, call variants, create consensus sequences appropriate for submission to public databases, and produce quality and lineage reports.
It will be a 1-day event introducing scalable and reproducible SARS-CoV-2 data analysis with Galaxy. People who are new to Galaxy can use existing Galaxy training materials to prepare ahead of the workshop. During the workshop, there will be live support in chat and live Q&A sessions, in which experts from NEB and the Galaxy community will answer questions.
- WHEN: December 1, 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.
- INFRASTRUCTURE: European Galaxy server and the Galaxy Training Material. Both will stay accessible and open after the training.
- CONTACT: Get in touch if you have questions.
Program & Material
This workshop has both live and virtual/asynchronous components. Training sessions are pre-recorded with most materials provided in advance in the program below.
Whenever you’re ready to get started, you can access training material by clicking in the program on the different icons:
- for slide deck for a lecture
- for hands-on tutorial (on the Galaxy Training Material)
- for video (accompanying a lecture, a tutorial or a demo)
- for shared Galaxy history (on the European Galaxy server)
Ahead of the Workshop - Introduction to Galaxy
Workshop Day (2021-12-01) - SARS-CoV-2 Data Analysis on Public Datasets
|Q & A||All experts||Info & Zoom link||Real-Time Q&A session (9 am CET)||1h|
|Galaxy for SARS-CoV-2 genome surveillance projects||Wolfgang Maier||/||Lecture: Get an overview of the workshop: production-ready Galaxy workflows for SARS-CoV-2 sequencing data, tools you should know to automate workflow execution, and how you combine all of it to turn Galaxy into a platform for genome-surveillance.||14m|
|Variant calling, reporting, consensus building (with Galaxy GUI)||Wolfgang Maier|| /
Part I / Complete
|Hands-on: Illumina or ONT, ampliconic or WGS data? Learn how to combine the right set of Galaxy workflows to analyze the type of SARS-CoV-2 sequencing data of your choice.||3h / 1h 30m|
|Q & A||All experts||Info & Zoom link||Real-Time Q&A session (4 pm CET)||1h|
After the Workshop - Scale up, Automation and Database Submission
|Accelerating Research Through Data Sharing||Carla Cummins||Lecture: Accelerating Research Through Data Sharing||13m|
|Variant calling, reporting, consensus building (with Galaxy CLI)||Simon Bray||/||Hands-on: Learn how to use the command line to upload your SARS-CoV-2 data to a Galaxy-server and launch workflows for its analysis. Note: This first step towards automation requires the command line tool Planemo for interacting with Galaxy if you want to follow along.||2h / 30m|
|The usegalaxy.eu SARS-CoV-2 bot in action||Wolfgang Maier||Demo: See in this demo how, on usegalaxy.*, we’ve used Planemo and Bioblend to build and operate an automated SARS-CoV-2 genome surveillance system based on the Galaxy workflows for variant calling, consensus building and reporting.||40m|
|Upload data to ENA||Miguel Roncoroni||/ /||Demo: Learn how to submit your sequencing data to the ENA directly from Galaxy.||1h / 10m|
|Upload data to a local datastore||Wolfgang Maier||Demo: So you’ve used Galaxy workflows to analyze your SARS-CoV-2 samples? Learn in this tutorial how to export results to your favorite datastore.||10m|
|Introduction to viral Beacon||Babita Singh||/||Demo: How to visualize tens of thousands of SARS-CoV-2 analysis results? Learn about the Viral Beacon project’s solution!||24m|
|Using and Customising ObservableHQ||Sergei Pond||Demo: In this demo you will get to know the ObservableHQ platform for interactive data visualization. You will see how covid19.galaxyproject.org uses it to build a dashboard for their SARS-CoV-2 analysis efforts and will learn how to customize this solution to fit your own purposes.||15m|
Optional extra training
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, supported by slide decks ().
Most of the tutorials are developed by the Galaxy Training Network. A feedback form is available at the bottom of each tutorial page. Please fill it out, it helps us to value and improve the tutorials.
- Histories: shared Galaxy history (), on the European Galaxy server, with all that you need to reproduce what is shown in the hands-on part.
- Demo: pre-recorded videos () demonstrating a technical point or a nice feature.
Most of the material is available already, and they will all stay available after the workshop. Most of the material have been developed by a community of people via the Galaxy Training Network. Some videos were recorded for different previous events, e.g. GTN Smörgåsbord or GCC2021 Training Week, and the captions were manually-curated by several community members.
Whenever you’re ready to get started, you can access the material by clicking on the different icons in the program!
Following the tutorials - Technical requirements
Some of you have asked about the technical requirements. You don’t need a specific operating system or software installed, all you need is a browser and internet connection.
To run the tutorials, you will need a Galaxy account. We recommend you to:
Register and use European Galaxy server.
You will receive an email to confirm your account before you can start using Galaxy.
Join the training event group, it will make your jobs go faster!
Support & 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.
Once you are in, you will see different channels (#general #random, #social), pass by and say hi to your colleagues!
When asking a question:
- Ask in the appropriate channel.
- Use threads.
- Say which server you’re using.
- Share all of the details (What did the tool say? What was the error? Did you see more information in the bug-report icon?).
During the workshop, the instructors will be there to reply to your questions.
If you need a certificate, you can request it at the end of the workshop. Please make sure to keep all the work, stay active in the discussions and fill out the final survey.
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|