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.

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Requirements

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

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Material

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

Introduction

Start here if you are new to microbiome analyses in Galaxy.

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Microbiome Analysis
Analyses of metagenomics data - The global picture

Metabarcoding / Amplicon analyses

Taxonomic characterisation of mixed samples using a single gene region.

Lesson Slides Hands-on Recordings Input dataset Workflows
16S Microbial analysis with Nanopore data
Antibiotic resistance detection
Building an amplicon sequence variant (ASV) table from 16S data using DADA2
help QIIME 2 Cancer Microbiome Intervention
help QIIME 2 Moving Pictures
16S Microbial Analysis with mothur (extended)
16S Microbial Analysis with mothur (short)

Metagenomics

Taxonomic and functional characterisation and assembly of mixed samples using whole genome data.

Lesson Slides Hands-on Recordings Input dataset Workflows
Assembly of metagenomic sequencing data
Binning of metagenomic sequencing data
Calculating α and β diversity from microbiome taxonomic data
Identification of the micro-organisms in a beer using Nanopore sequencing
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
Taxonomic Profiling and Visualization of Metagenomic Data

Metatranscriptomics

Taxonomic and functional characterisation of mixed samples using transcriptome data.

Lesson Slides Hands-on Recordings Input dataset Workflows
Metatranscriptomics analysis using microbiome RNA-seq data
Metatranscriptomics analysis using microbiome RNA-seq data (short)

Metaproteomics

These tutorials are step by step analysis from database generation to the discovery of peptides to verification, quantitation, and interpretation of the results.

Lesson Slides Hands-on Recordings Input dataset Workflows
Clinical Metaproteomics 1: Database-Generation
Clinical Metaproteomics 2: Discovery
Clinical Metaproteomics 3: Verification
Clinical Metaproteomics 4: Quantitation
Clinical Metaproteomics 5: Data Interpretation

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2
Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data

Frequently Asked Questions

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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

Contributors

This material was contributed to by:

Didier Debroas avatar Didier Debroasorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoTimothy J. Griffin avatar Timothy J. Griffinorcid logoHelena Rasche avatar Helena Rascheorcid logoDave Clements avatar Dave ClementsTarnima Omara avatar Tarnima Omaraorcid logoTeresa Müller avatar Teresa Müllerorcid logoBérénice Batut avatar Bérénice Batutorcid logoCristóbal Gallardo avatar Cristóbal GallardoSujai Kumar avatar Sujai Kumarorcid logoDeepti Varshney avatar Deepti VarshneyMatthias Bernt avatar Matthias Berntorcid logoNadia Goué avatar Nadia GouéBethan Manley avatar Bethan ManleyWillem de Koning avatar Willem de KoningKatherine Do avatar Katherine DoSiyu Chen avatar Siyu ChenDechen Bhuming avatar Dechen BhumingEmma Leith avatar Emma Leithorcid logoNikos Pechlivanis avatar Nikos PechlivanisPraveen Kumar avatar Praveen Kumarorcid logoPolina Polunina avatar Polina PoluninaSophia Hampe avatar Sophia Hampeorcid logoClea Siguret avatar Clea Siguretorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoBjörn Grüning avatar Björn Grüningorcid logoWolfgang Maier avatar Wolfgang MaierNuwan Goonasekera avatar Nuwan Goonasekeraorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoEngy Nasr avatar Engy NasrRay Sajulga avatar Ray Sajulgaorcid logoLinelle Abueg avatar Linelle Abuegorcid logoSubina Mehta avatar Subina Mehtaorcid logoPaul Zierep avatar Paul Zierep

Funding

These individuals or organisations provided funding support for the development of this resource

References