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
QIIME 2 Cancer Microbiome Intervention external-link
QIIME 2 Moving Pictures external-link
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 Metaproteiomics 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

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.

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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoBérénice Batut avatar Bérénice Batut orcid logoSaskia Hiltemann avatar Saskia Hiltemann orcid logoPaul Zierep avatar Paul Zierep

Contributors

This material was contributed to by:

orcid logoBert Droesbeke avatar Bert Droesbeke Emma Leith avatar Emma Leith Matthias Bernt avatar Matthias Bernt orcid logoLinelle Abueg avatar Linelle Abueg Willem de Koning avatar Willem de Koning orcid logoPratik Jagtap avatar Pratik Jagtap orcid logoNikos Pechlivanis avatar Nikos Pechlivanis orcid logoCristóbal Gallardo avatar Cristóbal Gallardo orcid logoPaul Zierep avatar Paul Zierep orcid logoDave Clements avatar Dave Clements orcid logoTimothy J. Griffin avatar Timothy J. Griffin Praveen Kumar avatar Praveen Kumar orcid logoHelena Rasche avatar Helena Rasche orcid logoNate Coraor avatar Nate Coraor Teresa Müller avatar Teresa Müller orcid logoBjörn Grüning avatar Björn Grüning Nuwan Goonasekera avatar Nuwan Goonasekera orcid logoNicola Soranzo avatar Nicola Soranzo Dechen Bhuming avatar Dechen Bhuming orcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solano Sophia Hampe avatar Sophia Hampe Niall Beard avatar Niall Beard orcid logoBérénice Batut avatar Bérénice Batut orcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulos orcid logoEngy Nasr avatar Engy Nasr orcid logoClea Siguret avatar Clea Siguret orcid logoSubina Mehta avatar Subina Mehta orcid logoSaskia Hiltemann avatar Saskia Hiltemann Ray Sajulga avatar Ray Sajulga Sujai Kumar avatar Sujai Kumar Katherine Do avatar Katherine Do Bethan Manley avatar Bethan Manley Siyu Chen avatar Siyu Chen Gildas Le Corguillé avatar Gildas Le Corguillé orcid logoPolina Polunina avatar Polina Polunina Deepti Varshney avatar Deepti Varshney orcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotz William Durand avatar William Durand orcid logoWolfgang Maier avatar Wolfgang Maier

Funding

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

References