Metagenomics

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

Requirements

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

Material

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

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 admin to access everything.

Maintainers

This material is maintained by:

Bérénice BatutBérénice Batut, Saskia HiltemannSaskia Hiltemann

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:

Bérénice BatutBérénice Batut, Saskia HiltemannSaskia Hiltemann, Dave ClementsDave Clements, Willem de KoningWillem de Koning, Pratik JagtapPratik Jagtap, Subina MehtaSubina Mehta, Ray SajulgaRay Sajulga, Emma LeithEmma Leith, Praveen KumarPraveen Kumar

References