Contact

 

 

Summer School Director: 
M. Pilar Francino
 
Summer School Administrator:
Kevin Cifuentes
Telf.: 961 925 911

 

 
 
 
 
 

 

SUMMER SCHOOL - Module 2

 

 

Module 2 /  Microbial Genomics and Metagenomics Workshop 

Dates: 26 Junio – 30 Junio 2023 

Organizazer: María Pilar Francino (francino_pil@gva.es)

You can check the program of the Summer School 2023.      

REGISTRATION

Module costs: 350 euros

Language: english

 

 

 

Instructors:

 

Giuseppe D’AuriaPhD. Scientist, FISABIO-PUBLIC HEALTH Genomics and Health Area and CIBERESP. Coordinator of FISABIO Sequencing and Bioinformatics Service (dauria_giu@gva.es).

M.Pilar FrancinoPhD. Scientist, FISABIO-PUBLIC HEALTH Genomics and Health Area and CIBERESP (francino_pil@gva.es).

Natalia IvanovaPhD. Scientist, JGI, Microbial Genomics & Metagenomics Scientific Program (nnivanova@lbl.gov).

 

 

David Páez, PhD. Associate Director of Discovery Informatics at Mammoth Biosciences (paezespino@gmail.com).

 

David Perez-Villarroya, MS. in Bioinformatics (pevida@alumni.uv.es).

 

Mariana Reyes, MS. in Genetics and Molecular and Cellular Biology, FISABIO-PUBLIC HEALTH, Bioinformatician at Sequencing and Bioinformatics Service (reyes_ber@gva.es).

 

Rekha Seshadri, PhD. Scientist, JGI, Microbial Genomics & Metagenomics Scientific Program (rseshadri@lbl.gov).

   

 

 

 

Module program:

 

Monday June 26th:

- 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 27th:

- 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 28th:

- 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

Lunch

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

 

 

Thursday June 29th:

- 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

Lunch

- 15:00 - 18:00 Preparation of student analysis projects: students form groups, choose their genome or metagenome analysis project and start carrying out

 

Friday June 30th:

- 09:00 - 11:00 Preparation of student analysis projects: students complete their genome or metagenome analysis project and prepare a presentation

Break

- 11:15 - 12:45 Presentations of genome or metagenome analysis projects by student groups

- 12:45 - 13:15 IMG Tutorial Summary, Discussion and Questions