Training courses: School of Python for genomics Massimiliano Orsini. Intermediate module: Analysing your genomic data with Python

Course Description

The use of Next-Generation Sequencing (NGS) has exponentially increased in the last two decades, both in the field of research and diagnostics. This technology allows obtaining millions of sequences (‘reads’) in a single experiment, making it possible to reconstruct complete genomes of pathogens relevant to public health in just a few hours. By that motivation, the Società Italiana di Diagnostica di Laboratorio Veterinaria (SIDiLV) and the Italian Infrastructure of Bioinformatics (IIB/ELIXIR Italy) organised the School of Python for genomics at the Italian National Institute of Health (ISS).
The School aims to provide the necessary skills to utilise the Python language both for the use and development of software and for genomics data analysis in general.

The whole School consists of 3 consequential modules:

1. Basic module: Introduction to Python programming (Nov 2022)
2. Intermediate module: Analysing your genomic data with Python (Jan-Feb 2024)
3. Hackathon module: Python programming for developers

The main objective of this second Module titled ‘Intermediate Module: Analysing your genomics data with Python’ will be to characterise a population of Escherichia coli strains through the analysis of Whole Genome Sequencing (WGS) data, identifying any groups of isolates that share epidemiological and/or genomic characteristics and the presence of specific virulence traits.

This module aims to achieve the following objectives:

• identify the distribution of serogroups of isolates
• analyse the presence and distribution of antibiotic-resistance genes
• examine the presence and distribution of virulence genes
• perform isolate typing (using methods such as MLST and cgMLST) and identify any correlations.

The course involves the development of a Python pipeline capable of processing raw data obtained from Illumina and/or Ion Torrent NGS.

Important Dates

• Deadline for applications: 9 January, 2024
• School date: 30 January - 2 February, 2024
  
  

Venue

Sapienza University of Rome
P.le Aldo Moro, 5
00195 Rome, Italy

Fee

No registration fee is required, but those who are selected will be expected to pay the SIDiLV membership fee for the year 2024 afterward (Full membership fee: 50 euros; Reduced membership fee for individuals under 35 years of age: 30 euros).
Participants are expected to pay their travel, meals, and hotel costs (if any).

Registration

Application Form

A maximum of 16 candidates will be selected based on a first-come, first-served basis, and the pre-requisites requested for attending the course, as emerging from the application form. Notifications of acceptance will be sent by January 10th.

Instructors

• Luca De Sabato - Dep. of Food Safety, Nutrition and Veterinary Public Health, National Institute of Health (SANV - ISS), Italy
• Arnold Knijn - Dep. of Food Safety, Nutrition and Veterinary Public Health, National Institute of Health (SANV - ISS), Italy
• Loredana Le Pera - Core Facilities Technical-Scientific Service, National Institute of Health (FAST - ISS), Italy
• Valeria Michelacci - Dep. of Food Safety, Nutrition and Veterinary Public Health, National Institute of Health (SANV - ISS), Italy
• Allegra Via - Sapienza University of Rome, Italy
  
  

Helpers

• Gianluca Frustagli - Core Facilities Technical-Scientific Service, National Institute of Health (FAST - ISS), Italy
• Chiara Pacelli - Institute for Biomedical Technologies of National Research Council (CNR-ITB), Italy
• Irene Ruspantini - Core Facilities Technical-Scientific Service, National Institute of Health (FAST - ISS), Italy
  
  

Prerequisites

This Intermediate Module is designed as a follow-up to the Basic Module of the School of Python, hence it assumes a basic understanding of programming and prior programming experience in Python as prerequisites. This Module will primarily focus on practical applications rather than theoretical concepts.

Target audience

Research scientists at any stage of their career who are using (or planning to use) genomic data in their research activities are welcome to attend the workshop.

Learning Outcomes

At the end of the course, the student will be able to:

• critically assess the quality of NGS data
• develop a complete pipeline for genomic analysis (starting from raw data to obtain final results).

In general, after completing the entire module, the student will have a greater awareness of both the use of Python and the impact that genomic analysis can have in a professional and social context.

Organisers

SIDiLV
ELIXIR Italy
Stefano Morabito - SIDiLV/ELIXIR Italy/National Institute of Health (ISS), Italy, Valeria Michelacci - SIDiLV/National Institute of Health (ISS), Italy, Loredana Le Pera - ELIXIR Italy (Training Platform)/National Institute of Health (ISS), Italy, Allegra Via - ELIXIR Italy (Training Platform)/Sapienza Univ. of Rome, Italy

Contact

For all kinds of queries, contact us at elixir.ita.training@gmail.com

Programme