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.

Registration is now open

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

After the Workshop - Scale up, Automation and Database Submission

Optional extra training

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, supported by slide decks ().

• Hands-on tutorials (): a step-by-step explanation, including all the required information, to perform a data analysis, often available also as pre-recorded video ().

  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.

Certificates

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