Metagenomics

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

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

Requirements

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

Material

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to metagenomics
plain text
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