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.

Requirements

Before diving into this topic, we recommend you to have a look at:

• Introduction to Galaxy Analyses

Material

Introduction

Start here if you are new to microbiome analyses in Galaxy.

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.

Other

Assorted Tutorials

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.

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Editorial Board

This material is reviewed by our Editorial Board:

Bérénice Batut

Saskia Hiltemann

Paul Zierep

For 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:

Subina Mehta

Cristóbal Gallardo

Polina Polunina

Teresa Müller

Bérénice Batut

Fotis E. Psomopoulos

Emma Leith

Ray Sajulga

Pratik Jagtap

Sophia Hampe

Nikolaos Pechlivanis

Paul Zierep

Dave Clements

QIIME2

Wolfgang Maier

Hans-Rudolf Hotz

Saskia Hiltemann

Siyu Chen

Praveen Kumar

Willem de Koning

Engy Nasr

Funders

This material was funded by:

Gallantries

EOSC-Life

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.