Microbiome analysis

This track explains the capability to analyze microbiome data using Galaxy, covering essential tasks such as amplicon analysis and its visualization. It progresses to more advanced topics, including assembly and binning - the requirements for reconstructing Metagenome-Assembled Genomes (MAGs) from microbiome samples, and finally extends to complex analyses like metatranscriptome studies and pathogen detection. Start with the tutorial at your own pace. If you need support contact us via the Slack Channel gta_microbiome. 🚨 The workflows used for this track where tested thoroughly on the EU server, if you encounter any issues with execution on other servers, we recommend to retry the tutorial on usegalaxy.eu!

Organiser(s) orcid logoPaul Zierep avatar Paul Ziereporcid logoBérénice Batut avatar Bérénice Batut
Instructor(s) orcid logoAnna Syme avatar Anna Symeorcid logoBérénice Batut avatar Bérénice Batutorcid logoEngy Nasr avatar Engy NasrGareth Price avatar Gareth PriceIgor Makunin avatar Igor MakuninMatthias Bernt avatar Matthias Berntorcid logoPaul Zierep avatar Paul Ziereporcid logoPolina Polunina avatar Polina Poluninaorcid logoRand Zoabi avatar Rand Zoabiorcid logoSaim Momin avatar Saim Mominorcid logoPratik Jagtap avatar Pratik Jagtap

Need help with these tutorials?

Open Slack support channel for this track:   #gta_microbiome

Introduction

Introduction to Microbiome Analysis.

Lesson Slides Hands-on Recordings
Introduction to Microbiome Analysis

Metabarcoding

Identify and analyze the diversity of species in environmental samples by amplifying and sequencing specific genetic markers

Lesson Slides Hands-on Recordings
Building an amplicon sequence variant (ASV) table from 16S data using DADA2
metabarcoding 16S microgalaxy

Metagenomics

Assemble, bin, and profile the taxonomic diversity using collective DNA from environmental samples. 🚨 The interactive tools Pavian and Phinch are currently not working on usegalaxy.org/org.au and .fr. Please use usegalaxy.eu for this step.

Lesson Slides Hands-on Recordings
Assembly of metagenomic sequencing data
assembly metagenomics microgalaxy
Binning of metagenomic sequencing data
binning metagenomics microgalaxy
Taxonomic Profiling and Visualization of Metagenomic Data
metagenomics taxonomic profiling microgalaxy
Calculating α and β diversity from microbiome taxonomic data
metagenomics diversity

Metatranscriptomics

Profile the taxonomic diversity and the functional processes from collective RNA from environmental samples

Lesson Slides Hands-on Recordings
Metatranscriptomics analysis using microbiome RNA-seq data
metatranscriptomics microgalaxy

Pathogen detection

Detect and track pathogens from metagenomic Nanopore sequencing

Lesson Slides Hands-on Recordings
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
microgalaxy Nanopore data analysis Pathogens detection Phylogenetic tree Heatmap cyoa