WHOCC Bioinformatics Training

Cambodia Training

Practical Information

Dates
10-15 October 2022
Infustracture:

Galacy Australia Training Server

Organized by:
WHO Collaborating Centre for Influenza, VIRDL, Melbourne Health
Contact:
Add to Google Calendar Add to Outlook Add to Office 365

Program

Below you will find all the tutorials for this course, everything you need to follow this course is listed here.

Please install the following software

Session 1: From Wet to Dry - Overview of NGS Technology

Objectives:

DNA Sequencing - Definition, Principle, Steps, Types, Uses

Title: DNA Sequencing - Definition, Principle, Steps, Types, Uses
1 Types of Sequencing link
2 Overview of NGS technology link

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

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:
Go to the video page to see all versions.

Speaker

Resources on bioinfo file formats

Title: Resources on bioinfo file formats
Sequence file formats link
Sequence file formats vcf and gff link

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

Understanding the output of Illumina/ONT

Title: Understanding the output of Illumina/ONT
Illumina ncl2fastq2 pdf link
ONT link

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

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:
Go to the video page to see all versions.

Speaker

Session 2: From Reads to Trees

Objectives:

Lecture Video

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
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

In this tutorial you will get some hand-on experience performing a quality assessment on sequencing data.
Length: 1 hour 10 minutes
Captions: Bérénice Batut, Nadia Goué, Saskia Hiltemann
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
Go to the video page to see all versions.

Speaker

Lecture Video

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
Go to the video page to see all versions.

Speaker

Tutorial Video

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:
Learning Objectives:
  • You will learn what mapping is
  • A genome browser is shown that helps you to understand your data
Go to the video page to see all versions.

Speaker

selfstudy tutorial

Self-study Tutorial

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!
image indicating this is a self-study session.
Tutorial:
Material: GTN Tutorial
Support:

Introduction to Reference Based Assembly

Title: Introduction to Reference Based Assembly
Video link

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

Self-study Tutorial

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!
image indicating this is a self-study session.
Tutorial: From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
Material: GTN Tutorial
Support:

Self-study Tutorial

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!
image indicating this is a self-study session.
Tutorial: Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
Material: GTN Tutorial
Support:

Introduction to Phylogenetics

Title: Introduction to Phylogenetics
Video link
EMBL Online Course on Phylogenetics link
How to read a phylogenetic tree by Andrew Rambaut link

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

Self-study Tutorial

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!
image indicating this is a self-study session.
Tutorial: Tree thinking for tuberculosis evolution and epidemiology
Material: GTN Tutorial
Support:

Session 3: From Noice to Proficent - What next?

Objectives

Self-study Tutorial

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!
image indicating this is a self-study session.
Tutorial: Creating, Editing and Importing Galaxy Workflows
Material: GTN Tutorial
Support:

Self-study Tutorial

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!
image indicating this is a self-study session.
Tutorial: Using dataset collections
Material: GTN Tutorial
Support:

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:
Go to the video page to see all versions.

Speaker

Lecture Video

Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.
Length: 15 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
Go to the video page to see all versions.

Speaker

selfstudy tutorial

Self-study Tutorial

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!
image indicating this is a self-study session.
Tutorial:
Material: GTN Tutorial
Support:

The Carpentries

Title: The Carpentries
Software Carpentries link
Data/Genomics Carpentries link
HPC Carpentries link

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

Wrap-up

Thanks for joining this course!

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Let us know what you thought of this course!

Please share your thoughts, suggestions, complaints and compliments with us in one of the following ways:

  • About this event: Please fill out this Feedback Form to help us improve this event in the future!
  • About the Materials (slides, training manuals): use the feedback forms at the end of the tutorial on the GTN website.
  • Anything else? - Let us know in Slack (#feedback )

Resource for the future

Title: Resource for the future
Galaxy Training Network link
GTN SmörgÄsbord link
Galaxy Community Conference link
Galaxy Community Conference 2023 link
Carpentries for Genomics link
Carpentries for Software R and Python link

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



Acknowledgements

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