Microbiome

A microbiome is the community of microorganisms that can usually be found living together in any given habitat. Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples.

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 Microbiome Analysis
16S Microbial Analysis with mothur (extended)
16S Microbial Analysis with mothur (short)
16S Microbial analysis with Nanopore data
Analyses of metagenomics data - The global picture
Antibiotic resistance detection
Assembly of metagenomic sequencing data
Binning of metagenomic sequencing data
Identification of the micro-organisms in a beer using Nanopore sequencing
Metatranscriptomics analysis using microbiome RNA-seq data
Metatranscriptomics analysis using microbiome RNA-seq data (short)
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
QIIME 2 Cancer Microbiome Intervention external-link
Taxonomic Profiling and Visualization of Metagenomic Data

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 logoBérénice Batut avatar Bérénice Batutorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoPaul Zierep avatar Paul Zierep

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:

Sophia Hampe avatar Sophia Hampeorcid logoDave Clements avatar Dave ClementsWillem de Koning avatar Willem de Koningorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoPaul Zierep avatar Paul Ziereporcid logoEngy Nasr avatar Engy Nasrorcid logoSaskia Hiltemann avatar Saskia HiltemannPraveen Kumar avatar Praveen Kumarorcid logoBérénice Batut avatar Bérénice BatutRay Sajulga avatar Ray SajulgaEmma Leith avatar Emma Leithorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoCristóbal Gallardo avatar Cristóbal GallardoQIIME2 avatar QIIME2Teresa Müller avatar Teresa Müllerorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoPolina Polunina avatar Polina Poluninaorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoNikolaos Pechlivanis avatar Nikolaos PechlivanisSiyu Chen avatar Siyu Chenorcid logoSubina Mehta avatar Subina Mehta

Funders

This material was funded by:

EOSC-Life avatar EOSC-LifeGallantries: Bridging Training Communities in Life Science, Environment and Health avatar Gallantries

References