Metagenomics data processing and analysis for microbiome

Comment: What is a Learning Pathway?
A graphic depicting a winding path from a start symbol to a trophy, with tutorials along the way
We recommend you follow the tutorials in the order presented on this page. They have been selected to fit together and build up your knowledge step by step. If a lesson has both slides and a tutorial, we recommend you start with the slides, then proceed with the tutorial.

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
Introduction to Microbiome Analysis

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
A short introduction to Galaxy
Galaxy Basics for genomics

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
Quality Control

Module 4: Assembly

This module covers the following questions:

Lesson Slides Hands-on Recordings
Assembly of metagenomic sequencing data

Module 5: Community taxonomic profiling

This module covers the following questions:

This module will cover taxonomic profiling in theory and also with an example tutorial.

Lesson Slides Hands-on Recordings
Taxonomic Profiling and Visualization of Metagenomic Data
Identification of the micro-organisms in a beer using Nanopore sequencing

Module 6: Taxonomic binning

This module covers the process used to classify DNA sequences obtained from metagenomic sequencing into discrete groups, or bins, based on their similarity to each other.

Lesson Slides Hands-on Recordings
Binning of metagenomic sequencing data

Module 8: Applying concepts to metatranscriptomics data

This module covers the following questions:

Lesson Slides Hands-on Recordings
Metatranscriptomics analysis using microbiome RNA-seq data

Lesson Slides Hands-on Recordings
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoBérénice Batut avatar Bérénice Batut


This material was funded by:

Gallantries: Bridging Training Communities in Life Science, Environment and Health avatar Gallantries