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 () and 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
16S Microbial Analysis with mothur (extended)
16S Microbial Analysis with mothur (short)
16S Microbial analysis with Nanopore data
nanopore
Analyses of metagenomics data - The global picture
Antibiotic resistance detection
nanopore plasmids assembly amr
Assembly of metagenomic sequencing data
assembly metagenomics
Identification of the micro-organisms in a beer using Nanopore sequencing
nanopore beer citizen science metagenomics
Introduction to metagenomics
Metatranscriptomics analysis using microbiome RNA-seq data
metatranscriptomics
Metatranscriptomics analysis using microbiome RNA-seq data (short)
metatranscriptomics
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
Nanopore data analysis Pathogens detection Phylogenetic tree Heatmap cyoa
Taxonomic Profiling and Visualization of Metagenomic Data
metagenomics taxonomic profiling

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.

Editorial Board

This material is reviewed by our Editorial Board:

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:

AvatarRay Sajulgaorcid logoAvatarPolina Poluninaorcid logoAvatarCristóbal GallardoAvatarEmma Leithorcid logoAvatarPaul ZierepAvatarTeresa MüllerAvatarPraveen Kumarorcid logoAvatarWolfgang Maierorcid logoAvatarDave Clementsorcid logoAvatarSubina MehtaAvatarWillem de Koningorcid logoAvatarBérénice Batutorcid logoAvatarPratik Jagtaporcid logoAvatarHans-Rudolf Hotzorcid logoAvatarEngy NasrAvatarSophia HampeAvatarSiyu Chenorcid logoAvatarSaskia Hiltemann

Funders

This material was funded by:

AvatarEOSC-LifeAvatarErasmus+ Programme

References