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.
For any question or discussions related to this topic, or to connect with others in the community, please visit the community chat:
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
You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.Introduction
Start here if you are new to microbiome analyses in Galaxy.
Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
---|---|---|---|---|---|
Introduction to Microbiome Analysis
|
|||||
Analyses of metagenomics data - The global picture |
Metabarcoding / Amplicon analyses
Taxonomic characterisation of mixed samples using a single gene region.
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) |
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 ZierepContributors
This material was contributed to by:
Paul Zierep Engy Nasr Clea Siguret Matthias Bernt Fotis E. Psomopoulos Cristóbal Gallardo QIIME2 Siyu Chen Bérénice Batut Nikos Pechlivanis Willem de Koning Teresa Müller Hans-Rudolf Hotz Dave Clements Polina Polunina Ray Sajulga Sophia Hampe Praveen Kumar Wolfgang Maier Subina Mehta Saskia Hiltemann Pratik Jagtap Emma LeithFunding
These individuals or organisations provided funding support for the development of this resource
References
- 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.