Microbiome
A microbiome is the community of microorganisms that can usually be found living together in any given habitat. Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples.
You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.Requirements
Before diving into this topic, we recommend you to have a look at:
Not sure where to start?
Try the Microbiome Learning Pathway! Start Learning
Material
Introduction
Start here if you are new to microbiome analyses in Galaxy.
Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
---|---|---|---|---|---|
Analyses of metagenomics data - The global picture |
Metabarcoding / Amplicon analyses
Taxonomic characterisation of mixed samples using a single gene region.
Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
---|---|---|---|---|---|
16S Microbial analysis with Nanopore data | |||||
Antibiotic resistance detection | |||||
QIIME 2 Cancer Microbiome Intervention external-link | |||||
QIIME 2 Moving Pictures external-link | |||||
16S Microbial Analysis with mothur (extended) | |||||
16S Microbial Analysis with mothur (short) |
Metagenomics
Taxonomic and functional characterisation and assembly of mixed samples using whole genome data.
Metatranscriptomics
Taxonomic and functional characterisation of mixed samples using transcriptome data.
Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
---|---|---|---|---|---|
Metatranscriptomics analysis using microbiome RNA-seq data | |||||
Metatranscriptomics analysis using microbiome RNA-seq data (short) |
Other
Assorted Tutorials
Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
---|---|---|---|---|---|
Introduction to Microbiome Analysis
|
Galaxy instances
You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.
You can also use the following Docker image for these tutorials:
docker run -p 8080:80 quay.io/galaxy/metagenomics-training
NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.
It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.
Frequently Asked Questions
Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.
Follow topic updates rss-feed with our RSS Feed
Editorial Board
This material is reviewed by our Editorial Board:
Bérénice Batut Saskia Hiltemann Paul ZierepFor any question related to this topic and the content, you can contact them or visit our Gitter channel.
Contributors
This material was contributed to by:
Polina Polunina Engy Nasr Pratik Jagtap Cristóbal Gallardo QIIME2 Ray Sajulga Sophia Hampe Wolfgang Maier Paul Zierep Bérénice Batut Emma Leith Praveen Kumar Saskia Hiltemann Dave Clements Nikolaos Pechlivanis Fotis E. Psomopoulos Subina Mehta Willem de Koning Siyu Chen Hans-Rudolf Hotz Teresa MüllerFunders
This material was funded by:
Gallantries EOSC-LifeReferences
- Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD.: Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology
- Pablo Yarza, Pelin Yilmaz, Elmar Pruesse, Frank Oliver Glöckner, Wolfgang Ludwig, Karl-Heinz Schleifer, William B. Whitman, Jean Euzéby, Rudolf Amann, Ramon Rosselló-Móra: Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences.