GTN Learning Pathway

Metagenomics data processing and analysis for microbiome
This learning path aims to teach you the basics of Galaxy and analysis of metagenomics data. You will learn how to use Galaxy for analysis, and will be guided through the common steps of microbiome data analysis: quality control, taxonomic profiling, taxonomic binning, assembly, functional profiling, and also some applications
Module 1: Introduction to metagenomics
Why study the microbiome? What are the different approaches for metagenomics? This module will give you a short introduction to metagenomics.
Lesson | Slides | Hands-on | Recordings |
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Introduction to metagenomics
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Module 2: Introduction to Galaxy
Get a first look at the Galaxy platform for data analysis. We start with a short introduction (video slides & practical) to familiarize you with the Galaxy interface, and then proceed with a slightly longer introduction tutorials where you perform a first, very simple, analysis.
Lesson | Slides | Hands-on | Recordings |
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A short introduction to Galaxy | |||
Galaxy 101
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Module 3: Quality control
When analysing sequencing data, you should always start with a quality control step to clean your data and make sure your data is good enough to answer your research question.
Lesson | Slides | Hands-on | Recordings |
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Quality Control
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Module 4: Assembly
This module covers the following questions:
- Why metagenomic data should be assembled?
- What is the difference between co-assembly and individual assembly?
- What is the difference between reads, contigs and scaffolds?
- How tools based on De Bruijn graph work?
- How to assess the quality of metagenomic data assembly?
Lesson | Slides | Hands-on | Recordings |
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Assembly of metagenomic sequencing data |
Module 5: Community taxonomic profiling
This module covers the following questions:
- Which species (or genera, families, …) are present in my sample?
- What are the different approaches and tools to get the community profile of my sample?
- How can we visualize and compare community profiles?
This module will cover taxonomic profiling in theory and also with an example tutorial.
Lesson | Slides | Hands-on | Recordings |
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Taxonomic Profiling and Visualization of Metagenomic Data | |||
Identification of the micro-organisms in a beer using Nanopore sequencing |
Module 8: Applying concepts to metatranscriptomics data
This module covers the following questions:
- How to analyze metatranscriptomics data?
- What information can be extracted of metatranscriptomics data?
- How to assign taxa and function to the identified sequences?
Lesson | Slides | Hands-on | Recordings |
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Metatranscriptomics analysis using microbiome RNA-seq data |
Recommended follow-up tutorials
Lesson | Slides | Hands-on | Recordings |
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Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition |
Editorial Board
This material is reviewed by our Editorial Board:
Funders
This material was funded by:
