e-learning
Taxonomic Profiling and Visualization of Metagenomic Data
Abstract
The term "microbiome" describes "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity".
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- 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?
Learning Objectives
- Explain what taxonomic assignment is
- Explain how taxonomic assignment works
- Apply Kraken and MetaPhlAn to assign taxonomic labels
- Apply Krona and Pavian to visualize results of assignment and understand the output
- Identify taxonomic classification tool that fits best depending on their data
Licence: Creative Commons Attribution 4.0 International
Keywords: Microbiome, metagenomics, microgalaxy, taxonomic profiling
Target audience: Students
Resource type: e-learning
Version: 4
Status: Active
Prerequisites:
Introduction to Galaxy Analyses
Learning objectives:
- Explain what taxonomic assignment is
- Explain how taxonomic assignment works
- Apply Kraken and MetaPhlAn to assign taxonomic labels
- Apply Krona and Pavian to visualize results of assignment and understand the output
- Identify taxonomic classification tool that fits best depending on their data
Date modified: 2024-06-14
Date published: 2023-05-03
Scientific topics: Metagenomics, Microbial ecology, Taxonomy, Sequence analysis
Activity log
