Module 1 / Microbial Genomics & Metagenomics Workshop

Dates: June 9th - June 13th 2025

Organiser: María Pilar Francino (pilar.francino@fisabio.es)

The workshop is addressed to students and professionals of biology, biomedical
research, the health sciences and related fields who are interested in learning and
sharing concepts, tools and research results in genomics, metagenomics and the
human microbiome. The workshop will train participants in state-of-the-art
analytical methods in this area, by means of theoretical lectures and seminars as
well as practical hands-on sessions in bioinformatics and biostatistics. Several
sessions will be devoted to training in the use of the Integrated Microbial Genomes
system (IMG), a database and analysis platform developed at the U.S. DOE Joint
Genome Institute (Berkeley, California) for comprehensive studies of genomes
and metagenomes. The IMG system will be presented by Dr. Natalia Ivanova and
Dr. Rekha Seshadri from the JGI's Microbial Genomics & Metagenomics Scientific
Program, the group responsible for IMG development.

Language: English

Module costs: 350 euros

Registration

You can check the program

Instructors

Module program

Monday June 9th

09:00 - 10:00 Welcome and Overview of the Workshop by Dr. M. Pilar Francino, Dr. Rekha Seshadri and Dr. Natalia Ivanova.
10:00 - 11:00 Features and Diversity of Microbial Genomes by Dr. M. Pilar Francino.

Break

11:15 - 12:15 Microbial communities, the human microbiome and its relationship to health by Dr. M. Pilar Francino.
12:15 - 13:15 Introduction to the Analysis of Bacterial Communities by Dr. M. Pilar Francino.

Lunch

15:00 - 15:30 Introduction to the Integrated Microbial Genomics system by Dr Natalia Ivanova.
15:30 - 18:00 Unix commands and moving around the system by David Pérez-Villarroya.

Tuesday June 10th

09:00 - 10:00 Informatic Processing and Quality Control of Sequencing Reads by Dr. Mariana Reyes.
10:00 - 11:00 Microbial Diversity Analyses with 16S rRNA (I) by Dr. Mariana Reyes.

Break

11:15 - 13:15 Microbial Diversity Analyses with 16S rRNA (II) by Dr. Mariana Reyes.

Lunch

15:00 - 18:00 Sequence Assembly and Read Mapping by Dr. Giuseppe D'Auria.

Wednesday June 11th

09:00 - 11:00 Functional Annotation and Comparative Genomics in IMG by Dr. Rekha Seshadri and Dr. M. Pilar Francino.

- Introduction

- Isolate Comparative Genomics Case Study: Live Demo 

Break   

11:15 - 13:15 Hands-on Exercise (student work). Review/Discuss solutions.

Lunch

15:00 - 18:00 CRISPR analyses and Uncovering the Earth's virome by Dr. David Páez-Espino. 

Thursday June 12th

09:00 - 11:00 IMG/M Metagenome Analysis: Live Demonstration by Dr. Natalia Ivanova and Dr. M. Pilar Francino.

  - Introduction

  - Metagenome Comparisons Case Study: Live Demo

Break

11:15 - 13:15 Hands-on Exercise (student work). Review/Discuss solutions.

Lunch

15:00 - 18:00 Preparation of student analysis projects: students form groups, choose their genome or metagenome analysis project and start carrying it out, (supervised by Dr. Rekha Seshadri and Dr. M. Pilar Francino).

Friday June 13th

09:00 - 11:00 Preparation of student analysis projects: students complete their genome or metagenome analysis project and prepare a presentation (supervised by Dr. Rekha Seshadri and Dr. M. Pilar Francino).

Break

11:15 - 12:45 Presentations of genome or metagenome analysis projects by student groups (supervised by Dr. Rekha Seshadri and Dr. M. Pilar Francino).

12:45 - 13:15 IMG Tutorial Summary and Discussion and Questions by Dr. M. Pilar Francino.