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
Introduction to metagenomics
slides
16S Microbial Analysis with mothur (extended)
tutorial
16S Microbial Analysis with mothur (short)
tutorial
16S Microbial analysis with Nanopore data
tutorial
Analyses of metagenomics data - The global picture
tutorial
Antibiotic resistance detection
tutorial
Metatranscriptomics analysis using microbiome RNA-seq data
plain text tutorial
Metatranscriptomics analysis using microbiome RNA-seq data (short)
tutorial

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.

Maintainers

This material is maintained by:

AvatarBérénice Batut AvatarSaskia 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:

AvatarBérénice Batut AvatarSaskia Hiltemann AvatarDave Clements AvatarCristóbal Gallardo AvatarWillem de Koning AvatarPratik Jagtap AvatarSubina Mehta AvatarRay Sajulga AvatarEmma Leith AvatarPraveen Kumar

References