Metagenomics data processing and analysis for microbiome

Comment: What is a Learning Pathway?

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.

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.

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.

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?

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.

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.

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?

Recommended follow-up tutorials