Module 2 / Basic Computational Skills for Genomic Analysis

Dates: June 16th - June 20th

Coordinator: Giuseppe D'Auria (giuseppe.dauria@fisabio.es)

The course is addressed to students and professionals of biology, biomedical
research, the health sciences and related fields who are interested in learning the
basic computational skills required to pursue their own genomic analyses. The
module will be eminently practical and hands-on and will teach participants skills
ranging from the installation and basic use of Linux systems to the building of
analysis pipelines for microbial genomics. Theoretical lectures and practical
hands-on sessions will be taught by Fisabio researchers and informaticians.

Official language: English

Module costs: 350 euros

Central Europe Time

Registration

You can check the program

Instructors

Module program

Monday, 16/06/2025

09:15 - 10:00 Next generation sequencing technologies: the birth of the Genomics Era (Rosario Gil).

10:00 - 10:45 Comparative genomics for genome annotation and functional analysis (Rosario Gil).

Break

11:00 - 11:45 NGS in microbial ecology (Taxonomy and metagenomics) (Rosario Gil).

11:45 - 13:00 Linux system, installing a new distro I (Pascual Asensi).

Lunch

14:30 - 17:00 Linux system, installing a new distro II (Pascual Asensi).

17:00 - 17:30 From office automation to computation for NGS (Giuseppe D'Auria).

Tuesday, 17/06/2025

09:00 - 10:45 Unix commands, moving around the system, practice (David Perez Villarroya).

Break

11:00 - 12:00 One command line pipelines, practice (David Perez-Villarroya).

12.00 - 13.00 NGS Bioinformatics formats, managing data (David Perez-Villarroya).

Lunch

14.30 - 16.00 NGS Bioinformatics formats, managing data, practice (David Perez Villarroya).

16:00 - 16:30 Microbial genome assembly and mapping (Giuseppe D'Auria).

16:30 - 17:30 Microbial genome assembly, practice I (Giuseppe D'Auria).

Wednesday, 18/06/2025

09:00 - 10:45 Microbial genome assembly, practice II (Giuseppe D'Auria).

Break 

11:00 - 12:00 Microbial genome assembly, manual edition (Giuseppe D'Auria).

12:00 - 13:00 Microbial genomics annotation (Giuseppe D'Auria).

Lunch

14:30 - 15:30 Microbial genome mapping (Giuseppe D'Auria).

15:30 - 16:30 Microbial SNPs/InDels analysis (Giuseppe D'Auria).

16:30 - 17:30 Microbial transcriptomics and differential analysis (Mariana Reyes).

Thursday, 19/06/2025

09:00 - 10:45 Microbial comparative genomics overview (Mariana Reyes).

Break

11:00 - 12:00 Comparative genomics and pangenome reconstruction (Mariana Reyes).

12:00 - 13:00 Comparative SNPs/InDels analysis and phylogenetic reconstructions I (Mariana Reyes).

Lunch

14:30 - 15:30 Comparative SNPs/InDels analysis and phylogenetic reconstructions II (Mariana Reyes).

15:30 - 17:30 Insight into metabolic networks reconstructions metaDAG (Mariana Reyes).

Friday, 20/06/2025

09:00 - 10:00 NGS sequencing and beyond (Rosario Gil).

09:45 - 10:45 Creating scripts and pipelines (Giuseppe D'Auria).

Break

11:00 - 12:00 Students projects (Mariana Reyes).

12:00 - 13:00 Questionnaires and closure (Giuseppe D'Auria).