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 Galaxy servers
Analyses of metagenomics data - The global picture
tutorial
Antibiotic resistance detection tutorial
  • 16S Microbial Analysis with mothur (extended)
    tutorial
    Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition tutorial
    Metatranscriptomics analysis using microbiome RNA-seq data (short) tutorial
    Identification of the micro-organisms in a beer using Nanopore sequencing tutorial
    Assembly of metagenomic sequencing data tutorial
    16S Microbial analysis with Nanopore data tutorial
    16S Microbial Analysis with mothur (short)
    tutorial
  • Metatranscriptomics analysis using microbiome RNA-seq data plain text tutorial
  • Introduction to metagenomics
    plain text
  • 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:

    orcid logoAvatarBérénice Batutorcid logoAvatarSaskia 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:

    orcid logoAvatarSaskia HiltemannAvatarTeresa MüllerAvatarSiyu ChenAvatarPraveen Kumarorcid logoAvatarEngy Nasrorcid logoAvatarSubina MehtaAvatarRay Sajulgaorcid logoAvatarPolina Poluninaorcid logoAvatarBérénice BatutAvatarCristóbal GallardoAvatarWillem de KoningAvatarEmma LeithAvatarDave ClementsAvatarPratik Jagtap

    References