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.
| Organisers(s) |
 
Paul Zierep
Bérénice Batut
|
| Instructor(s) |
Bérénice Batut
Paul Zierep
Matthias Bernt
Polina Polunina
Engy Nasr
Rand Zoabi
|
Introduction
Introduction to Microbiome Analysis.
| Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|
|
Introduction to Microbiome Analysis
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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 | |||
| MGnify amplicon workflow |
Tutorial (will come soon) |
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Metagenomics
Assemble, bin, and profile the taxonomic diversity using collective DNA from environmental samples
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
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 |