Module 2 / Microbial Genomics & Metagenomics Workshop

Dates: June 24th - June 28th 2024

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.

Module costs: 350 euros

Language: english

Registration

You can check the program

Instructors

Module program

Monday June 24th

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 25th

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

Break

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

Lunch

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

Wednesday June 26th

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

- Introduction

- Isolate Comparative Genomics Case Study: Live Demo 

Break   

11:15 - 13:15   - Hands-on Exercise (student work)

- Review/Discuss solutions by Dr. Rekha Seshadri and Dr. M. Pilar Francino 

Lunch

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

Thursday June 27th

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

  - Introduction

  - Metagenome Comparisons Case Study: Live Demo

Break

11:15 - 13:15  - Hands-on Exercise (student work)

  - Review/Discuss solutions by Dr. Natalia Ivanova and Dr. M. Pilar Francino

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 28th

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, Discussion and Questions, supervised by Dr. M. Pilar Francino