Metagenomics is a discipline that enables the genomic study of uncultured microorganisms


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


Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
Introduction to metagenomics
16S Microbial Analysis with mothur (extended)
16S Microbial Analysis with mothur (short)
16S Microbial analysis with Nanopore data
Analyses of metagenomics data - The global picture
Antibiotic resistance detection
Metatranscriptomics analysis using microbiome RNA-seq data
plain text tutorial
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

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.


This material is maintained by:

AvatarBérénice BatutAvatarSaskia Hiltemann

For any question related to this topic and the content, you can contact them or visit our Gitter channel.


This material was contributed to by:

Bérénice BatutSaskia HiltemannDave ClementsCristóbal GallardoWillem de KoningPratik JagtapSubina MehtaRay SajulgaEmma LeithPraveen Kumar