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Giuseppe Defazio, Ph.D. edited this page Jul 3, 2026 · 24 revisions

ELIXIR-IIB Italy

Summer School - BARI - 29 June - 3 July 2026

Profiling of microbial communities using targeted and shotgun metagenomics

Course Lectures All the lectures shown during the course are available here.
Please note is not an open access folder so remember to ask to access it.

Program

Day 1 - June 29th

Time Learning Experience Topic
11:00 - 14:00 Welcome and registration
14:00 - 14:30 Welcome and short intro on ELIXIR Introduction to the course
14:30 - 17:30 Lecture What is metagenomics - metabarcoding vs shotgun
Intro on sequencing technologies
  • Second Generation Technologies
  • Third Generation Technologies
Introduction to DNA-metabarcoding
  • Historical notes
  • Applications: from the gut microbiome to food traceability
Experimental design
17:00 - 18:00 Hands-On Access to virtual machines and upload/download tests of files and folders
Setup of Colab account and Colab fundamentals

Day 2 - June 30th - Analysis of microbiome biodiversity through DNA metabarcoding

Time Learning Experience Topic
09:00 - 09:45 Lecture Amplicon sequencing: Variable regions vs full length - Prof. Bruno Fosso
9:45 - 10:30 Hands-On Characteristics of the raw sequencing data
  • Data visualization
  • Data quality: fastqc/multiqc.
  • Data import into qiime
  • Data pre-processing
10:30 - 11:00 Coffee Break
11:00 - 12:00 Lecture Prof. Bruno Fosso
  • Denoising vs OTU-clustering & Chimera removal
  • Taxonomic classification: Approaches based on similarity analysis vs Bayesian classifiers
12:00 - 13:00 Hands-On Dott. Giuseppe Defazio
  • Data Denoising
  • Taxonomic classification of data and visualization of relative abundances
13:00 - 14:00 Lunch Break
14:00 - 14:30 Questions & Answers
14:30 - 15:30 Lecture Prof. Bruno Fosso & Dott. Giuseppe Defazio
  • Theoretical notes on the concept of Diversity and Diversity measures
  • Data normalization for Rarefaction and CLR
  • Dimensional reduction approaches (PCoA/PCA) and permANOVA tests
  • Statistical tests on alpha diversity and beta diversity metrics
  • Differential Abundance Analysis
15:30 - 17:00 Hands-On Prof. Bruno Fosso & Dott. Giuseppe Defazio
  • Rarefaction and diversity metrics
  • Statistical Comparison
  • Differential Abundance Analysis

Day 3 - July 1st - Analysis of the taxonomic and functional composition of the microbiome through shotgun metagenomics

Time Learning Experience Topic
09:00 - 10:30 Lecture Dott. Claudio Donati
  • Brief introduction to the main analysis techniques:
    • Taxonomic profiling
    • Functional profiling
    • Metagenome assembly and binning
  • Computational tools for metagenomics
  • operating systems
  • hardware requests
  • software tools (nextflow-docker, etc)
10:30 - 11:00 Coffee Break
11:00 - 12:30 Lecture Dott. Claudio Donati
  • Taxonomic and functional profiling using shotgun dataRaw data preprocessing: read filtering and host elimination
  • Taxonomic profiling:- MetaPhlAn- Kraken2/Bracken
  • Functional profiling: HUMANN
  • Taxonomic profiling beyond the species level: Strain level analysis
  • The species concept in bacteria
  • Genomic variability within the species: strain, genome, pangenome
  • Strain level profiling: StrainPhlAn
12:30 - 13:30 Lunch Break
13:30 - 15:00 Hands-On Dott. Claudio Donati
  • MetaPhlAn
  • Kraken2/Bracken
  • HUMANN
    		•
    15:00 - 15:30 Coffee Break
    15:30 - 16:00 Hands-On Dott. Claudio Donati
      StrainPhlAn
    16:00 - 17:00 Lecture Dott. Claudio Donati
    • Metagenome assembly and binning
    • Binning- Quality measures for MAGs
    • Dereplication of MAGS- Taxonomic classification of MAGs
    • Taxonomic classification of MAGs
    • MAGs Taxonomic Classification with kMetaShot
    • Functional annotation of MAGs

    Day 4 - July 2nd - Machine Learning and Network Inference for Microbiome Data: Methods and Practice

    Time Learning Experience Topic
    09:00 - 10:30 Lecture Dott. Pierfrancesco Novielli & Dott. Michele Magarelli
    • Fundamentals of Machine Learning: problem formulations, model inputs/outputs, and the concept of learning from data
    • From data tables to model-ready features: representation choices and core preprocessing principles
    • Model assessment and validation: data splitting strategies, cross-validation, performance metrics, and control of leakage/confounding factors
    • Exploratory analyses: dimensionality reduction techniques and appropriate interpretation of embedded representations
    • SModel explainability: global versus local explanations, feature importance, and SHAP (scope, assumptions, and limitations)
    10:30 - 11:00 Coffee Break
    11:00 - 12:30 Hands-On Dott. Pierfrancesco Novielli & Dott. Michele Magarelli Practical workflow: from data tables to modelling and interpretation
    • Data import and initial inspection (feature table and metadata)
    • Construction of model inputs: basic QC, representation choices, and preprocessing within a reproducible pipeline
    • Baseline modelling and validation (cross-validation and performance metrics)
    • Model interpretation using explainability tools (feature importance and SHAP)
    12:30 - 13:30 Lunch Break
    13:00 - 15:00 Lecture Eugenio Parente - Inference of microbial association networks from metataxonomic data.
    • Associations vs interactions in microbiome science
    • A primer on network science terminology
    • Measuring networks: networks, node and edge statistics
    • Methods for the inference of association networks
    • Statistical and graphical tools for the analysis of microbial association networks
    15:00 - 15:30 Coffee Break
    15:30 - 17:00 Hands-On Inference of microbial association networks with R:
    • Data preparation and package installation
    • Inference of networks with NetCoMi and SpiecEasi
    • Calculation of network statistics
    • Postprocessing with tidygraph and ggraph

    Social BEER

    We will move to Le Officine Clandestine after the end of day 4 lecture/hands-on to have a very intensive session of networking (and beer/no-beer drinking :) ) in a very relaxed environment. We reserved starting by 18:30.

    Day 5 - July 3rd - Galaxy Project and usegalaxy.eu

    Tiass link
    Public history to the tutorial data

    Time Learning Experience Topic
    09:00 - 09:30 Lecture Dr. Mina Hojat Ansari - Introduction to Galaxy Project: Galaxy concepts & logic
    09:30 - 10:00 Hands-On Galaxy hands-on: sign-in, log-in, how-to
    10:00 - 11:00 Hands-On FAIRyMAGs workflow - part 1
    11:00 - 11:15 Coffee Break
    11:15 - 13:15 Hands-On FAIRyMAGs workflow - part 2
    13:15 - 13:30 Closing remarks Closing remarks from Summer School committee

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