Module: SARS-CoV-2 Data Analysis

This module covers the contents of the SARS-CoV-2 with Galaxy course, first run in August 2021

Introduction to Galaxy

Lecture & Demo Video

Description:

This video will introduce the Galaxy data analysis platform, and give a short demo on how to use it.
Length: 10 minutes
Captions: Anton Nekrutenko
Created: 15 February 2021
Materials:
Support:
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Speaker

Tutorial Video

Description:

This tutorial will introduce you to Galaxy. You will familiarize yourself with tools, workflows and histories. Those skills will be needed the next days
Length: 13 minutes
Captions: Saskia Hiltemann
Created: 21 July 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Familiarize yourself with the basics of Galaxy
  • Learn how to obtain data from external sources
  • Learn how to run tools
  • Learn how histories work
  • Learn how to create a workflow
  • Learn how to share your work
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Speaker

Demo Video

Description:

In this demo video, we will show how to perform an NGS data analysis, using a SARS-CoV-2 example dataset. If you would like to run the full tutorial yourself, please find the link below (duration 1h-1.5h).
Length: 15 minutes
Captions: Anton Nekrutenko
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
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Speaker

Data Upload & Quality Control

In this sesssion, we will walk you through the basics of quality checking your sequencing data. This session consists of a lecture followed by a hands-on tutorial.

Quality Control (Lecture)

Description:

This lecture goes over the concepts involved in assessing the quality of your sequencing data.
Length: 40 minutes
Captions: Yvonne Hiltemann, Nadia Goué, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
  • Assess long reads FASTQ quality using Nanoplot and PycoQC
  • Perform quality correction with Cutadapt (short reads)
  • Summarise quality metrics MultiQC
  • Process single-end and paired-end data
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Speaker

Quality Control (Tutorial)

Description:

In this tutorial you will get some hand-on experience performing a quality assessment on sequencing data.
Length: 50 minutes
Captions: Andrew Lonsdale
Created: 19 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
  • Assess long reads FASTQ quality using Nanoplot and PycoQC
  • Perform quality correction with Cutadapt (short reads)
  • Summarise quality metrics MultiQC
  • Process single-end and paired-end data
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Speaker

Go to session page.

In this sesssion, we will walk you through the basics of mapping your sequencing data to a reference genome. This session consists of a lecture followed by a hands-on tutorial.

Mapping (Lecture)

Description:

This lecture covers the basic concepts involved in mapping sequencing reads to a reference genome.
Length: 10 minutes
Captions: Daniel Blankenberg
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • You will learn what mapping is
  • A genome browser is shown that helps you to understand your data
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Speaker

Mapping (Tutorial)

Description:

In this tutorial you will map sequencing data to a reference genome, and explore the mapped reads in a genome browser.
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • You will learn what mapping is
  • A genome browser is shown that helps you to understand your data
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Speaker

Go to session page.

Tutorial Video

Length: 13 minutes
Captions: Delphine Lariviere
Created: 9 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Understand and master dataset collections
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Speaker

Removal of human reads from SARS-CoV-2 sequencing data

image indicating this is a self-study session. This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: Removal of human reads from SARS-CoV-2 sequencing data
Material: GTN Tutorial
Support:
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Instructor

SARS-CoV-2 Data Analysis on Public Datasets

Tutorial Video

Description:

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
Length: 13 minutes
Captions: Pia H.
Created: 9 August 2021
Support:
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Speaker

Tutorial Video

Length: 55 minutes
Captions: Wolfgang Maier
Created: 10 May 2023
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Discover and obtain recommended Galaxy workflows for SARS-CoV-2 sequence data analysis through public workflow registries
  • Choose and run a workflow to discover mutations in a batch of viral samples from sequencing data obtained through a range of different protocols and platforms
  • Run a workflow to summarize and visualize the mutation discovery results for a batch of samples
  • Run a workflow to construct viral consensus sequences for the samples in a batch
  • Know different SARS-CoV-2 lineage classification systems, and use pangolin and Nextclade to assign samples to predefined lineages
  • Combine information from different analysis steps to be able to draw appropriate conclusions about individual samples and batches of viral data
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Speaker

Tutorial Video

Description:

This is a more technical tutorial which will teach you how to run workflows from the command line and scale your analyses. If you are on Windows, you will need WSL/WSL2 setup before this session.
Length: 30 minutes
Captions: Simon Bray
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
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Speaker

Demo Video

Description:

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.
Length: 40 minutes
Captions: Helena Rasche
Created: 9 August 2021
Support:
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Speaker

Visualisation & Data Export

Accelerating Research through data sharing

Title: Accelerating Research through data sharing
Length: 13m
Video link
Author(s):

Speaker

Carla Cummins

Note: This is a training session outside of the GTN. Please contact the authors if you have questions.

Demo Video

Length: 10 minutes
Captions: Pia H., Assunta DeSanto
Created: 8 December 2021
Support:
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Speaker

Lecture & Tutorial Video

Description:

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.
Length: 10 minutes
Captions: Helena Rasche
Created: 9 August 2021
Support:
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Speaker

Demo Video

Description:

How to visualize tens of thousands of SARS-CoV-2 analysis results? Learn about the Viral Beacon project’s solution!
Length: 24 minutes
Captions: Assunta DeSanto
Created: 8 December 2021
Materials:
Support:
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Demo Video

Description:

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.
Length: 15 minutes
Captions: Assunta DeSanto
Created: 8 December 2021
Support:
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Speaker

Optional Extra Training

This session will introduce the SRA Aligned Read format, and show you how to use this in Galaxy to analyze a SARS-CoV-2 dataset.

SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis (Lecture)

Description:

This lecture will introduce the SRA Aligned Read format available in the cloud from SRA, as well as some accompanying metadata that can help you search and filter the data. This sessions is aimed specifically at SARS-CoV-2 runs in SRA.
Length: 15 minutes
Captions: Jonathan Trow
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Learn about SRA aligned read format and vcf files for Runs containing SARS-CoV-2 content
  • Understand how to search the metadata for these Runs to find your dataset of interest and then import that data in your preferred format
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Speaker

SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis (Tutorial)

Description:

This tutorial will walk you through accessing and using SRA Aligned read format in Galaxy.
Length: 40 minutes
Captions: Jonathan Trow
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Learn about SRA aligned read format and vcf files for Runs containing SARS-CoV-2 content
  • Understand how to search the metadata for these Runs to find your dataset of interest and then import that data in your preferred format
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Speaker

Go to session page.

Tutorial Video

Description:

This tutorial guides you through the preprocessing of sequencing data of bronchoalveolar lavage fluid (BALF) samples obtained from early COVID-19 patients in China. Since such samples are expected to be contaminated signficantly with human sequenced reads, the goal is to enrich the data for SARS-CoV-2 reads by identifying and discarding reads of human origin before trying to assemble the viral genome sequence.
Length: 25 minutes
Captions: Mehmet Tekman
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
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Speaker

Lecture & Demo Video

Description:

The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world’s population. Accurate and timely diagnosis of COVID-19 infection is an important step for providing care and containing its further spread. In this tutorial, attendees will be introduced to two workflows – a) database search workflow and b) peptide validation workflow. Attendees of the workshop will get an in-depth knowledge of the Galaxy workflows that detect SARS-CoV-2 peptides (10.1186/s12014-021-09321-1)) and co-infecting pathogen peptides (10.1021/acs.jproteome.0c00822).
Length: 35 minutes
Captions: Emma Leith
Created: 15 February 2021
Materials:
Support:
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Speakers

Scripting Galaxy using the API and BioBlend

image indicating this is a self-study session. This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: Scripting Galaxy using the API and BioBlend
Material: GTN Slides
Support:
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Instructor

Case Studies: What you can do with SARS-COV-2 data

Learn what you can do with SARS-CoV-2 data

Title: Case Studies: What you can do with SARS-COV-2 data
Description: Learn what you can do with SARS-CoV-2 data
Length: 32m
Video link
Author(s):

Speaker

Andrew Page

Note: This is a training session outside of the GTN. Please contact the authors if you have questions.