When and Where

3 - 7 February 2020
Stazione Zoologica Anton Dohrn
Naples, Italy

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Schedule

Schedule

 

Monday 03 February
9:00 – 9:15 Registration
9:15 – 9:30 Institutional welcome addresses
9:30 – 10:00 Introduction to the course and participant elevator talks
10:00 – 11:00 Introduction to Metabarcoding and Metagenomics
11:00 – 11:20 Coffee break
11:20 – 12:30 Reference resources and sequencing platforms
12:30 – 13:45 Lunch @ Punch&Judy
13:45 – 15:30 Unix hands on exercises and file formats
15:30 – 15:50 Coffee break
15:50 – 18:00 Unix hands on exercises (continue)
18:30 – 20:00 Welcome cocktail @ SZN Fresco room

Detailed contents Day 1
Registration, institutional welcome addresses and course introduction. Students will be registered and introduced to the main contents of the course. After the institutional talks, participants will be asked to introduce themselves with a short elevator talk.
Introduction to metagenomics, metabarcoding and bioinformatics. In this session, students will be introduced to the main concepts behind metabarcoding and metagenomics, with an overview on study design, sequencing technologies and bioinformatics. In the afternoon section, students will be introduced to *nix shells, connection to a remote host, command-line interface, bash-scripting, basic commands for file management, browsing, editing and manipulation dealing with main formats in forthcoming analyses (e.g. FASTQ and FASTA).
Trainers: Chiusano, Stefanni, Miralto, Sangiovanni

Tuesday 04 February
9:00 – 10:30 Overview of the metabarcoding approach
10:30 – 10:50 Coffee break
10:50 – 12:30 Basics on QIIME2, from data collection to taxonomic output (16S and 18S)
12:30 – 13:45 Lunch @ Punch&Judy
13:45 – 16:00 Advanced analyses on metabarcoding data: statistics and community composition analyses for ecological investigations with QIIME2
16:00 – 16:20 Coffee break
16:20 – 18:30 QIIME2 hands-on exercises for alpha- and beta-diversity analyses
Detailed contents Day 2
Introduction to metabarcoding. In this session, students will learn about metabarcoding, with a brief coverage of its history and basic concepts, gene markers, reference databases and pipelines. The class will be focused primarily on the widely used QIIME2 pipeline, and will detail differences between different approaches (e.g. denoising vs. OTU-picking). Students will run commands for analyses of both 16S and 18S metabarcoding data, from importing and checking raw sequencing data to the inference of the taxonomic structure and diversity of the analysed assemblages.
Core concepts introduced: metabarcoding, ecological analysis, marker genes, denoising, OTU-picking, alpha-diversity, beta-diversity, taxonomy.
Trainers: Piredda, Tangherlini
Wednesday 05 – February
9:00 – 10:30 Eukaryotic diversity using COI and other, non 18S-related, markers
10:30 – 10:50 Coffee break
10:50 – 12:30 Hands-on session on creating and utilizing custom reference datasets for metabarcoding
12:30 – 13:45 Lunch @ Punch&Judy
13:45 – 16:00 De novo shotgun data processing: from read assembly to genome binning
16:00 – 16:20 Coffee break
16:20 – 18:30 Data annotation and functional potential
Detailed contents Day 3
Metabarcoding with alternative marker genes. In this session, students will learn how to utilize non-standard marker genes in metabarcoding analyses. They will learn about strategies for the creation of custom reference databases for ad hoc analyses in eukaryotic metabarcoding analyses and for taxonomic inference (utilizing MEGAN and MALT).
Core concepts introduced: eukaryotic diversity, custom database, marker genes.
De novo shotgun data processing: from read assembly to genomic annotation. In this session, students will learn how to perform de novo shotgun sequence analysis to obtain relevant data about prokaryotic diversity from metagenomic data. In particular, they will perform metagenomic read assembly with MEGAHIT and genome binning with MetaBAT2. Genome bins will be screened using CheckM. High-quality bins will be kept and annotated with Prokka; annotated sequences will be further utilized to understand their potential function (using GraftM), possible production of secondary metabolites (with antiSMASH) and for further analyses.
Core concepts introduced: prokaryotic diversity, genome annotation, functional annotation, metabolic potential.
Trainers: Pasolli, Stanković, Stefanni, Tangherlini
Thursday 06 February
9:00 – 10:30 Shotgun data processing: mapping-based approaches for taxonomic and functional profiling at species and strain level resolution
10:30 – 10:50 Coffee break
10:50 – 12:30 Shotgun data processing: mapping-based approaches for taxonomic and functional profiling at species and strain level resolution (continue)
12:30 – 13:45 Lunch @ Punch&Judy
13:45 – 16:00 Shotgun data processing: mapping-based approaches for taxonomic and functional profiling at species and strain level resolution (continue)
16:00 – 16:20 Coffee break
16:20 – 18:30 Shotgun data processing: mapping-based approaches for taxonomic and functional profiling at species and strain level resolution (continue)
20:00 Social dinner @ Umberto
Detailed contents Day 4
Reference-based data processing: mapping approaches for taxonomic and functional profiling at species and strain level resolution. In this session, students will learn how to perform mapping-based taxonomic (with MetaPhlAn) and functional (HUMAnN) profiling of metagenomic reads and the use of the curatedMetagenomicData package. Moreover, they will see how to perform strain-level analyses based on StrainPhlAn, PanPhlAn and PhyloPhlAn.
Core concepts introduced: strain variation, reference data mapping, read mapping, functional profiling.
Trainers: Valles-Colomer, Zolfo
Friday 07 February
9:00 – 10:30 Keynote lecture by Duccio Cavalieri: “The microbiome, challenges and perspectives” Part I
10:30 – 10:50 Coffee break
10:50 – 11:50 Keynote lecture by Duccio Cavalieri: “The microbiome, challenges and perspectives” Part II
11:50 – 12:30 Brainstorming session, moderators: D. Cavalieri and M.L. Chiusano
“Genus, species, strain: Metagenomics and the evolution of modern taxonomy”
12:30 – 14:15 Lunch @ Punch&Judy
14:15 – 15:30 Discussion with the students on course results
15:30 – 16:30 Final comments and concluding remarks

Detailed contents Day 5
The Keynote lecture and the brainstorming sessions will be opened.
Brain storming session
Opinion, comments and observations on the proposed subject from the  students will be the starting point of the open discussion. They will feed the discussion with trainers and other participants concerning  the benefits and still open questions in the field of meta-omics  analyses.

Discussion with the students on course results
In the afternoon, the assessment of the final outcomes from previous  days’ work summarized in few slides from groups of students will also allow them to comment and pose questions to the trainers regarding  issues or themes just covered, offering the opportunity to discuss  about best practice in data representation and delivery.

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