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. Please note that the tutorials of this track where all tested successfully on useGalaxy.eu, therefore it is recommended to run all tools on this server !

Organisers(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 logoPratik Jagtap avatar Pratik Jagtap

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Open Slack support channel for this track: comment   #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

Metagenomics

Assemble, bin, and profile the taxonomic diversity using collective DNA from environmental samples

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

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

Metaproteomics

Generation and search of any metaproteomics database, verification and quantification of the proteins/peptides, statistical analysis of the quantified peptides

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

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