Dates: July 1st - July 5th
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 and the utilization of Qiime2 as platform for metataxonomy analysis. Theoretical lectures and practical hands-on sessions will be taught by FISABIO researchers and informaticians.
Official language: English.
Central Europe Time.
Module costs: 350 euros
Instructors
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Giuseppe D'Auria
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Pascual Asensi
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Rosario GIl
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Mariana Reyes
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David Perez-Villaroya
Course program
Monday, 01/07/2024
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)
Break
14:30 - 16:00 Linux system, installing a new distro II. (Pascual Asensi)
16:00 - 16:30 From office automation to computation for NGS. (Giuseppe D'Auria)
16:30 - 17:30 Unix commands, moving around the system, practice I. (David Perez Villarroya)
Tuesday, 02/07/2024
09:00 - 10:45 Unix commands, moving around the system, practice II. (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)
Break
14.30 - 15.30 NGS Bioinformatics formats, managing data, practice. (David Perez Villarroya)
15:30 - 16:30 Genome Assembly and mapping. (Giuseppe D'Auria) 16:30 - 17:30 Genome assembly, practice. (Giuseppe D'Auria)
Wednesday, 03/07/2024
09:00 - 10:45 Genome mapping, practice. (Giuseppe D'Auria)
Break
11:00 - 12:00 Qiime2: Introduction. How to install the environment, applications. (Mariana Reyes)
12:00 - 13:00 Qiime2: Data formats and operations. (Mariana Reyes)
Break
14:30 - 15:30 Qiime2: Hands-on section. (Mariana Reyes)
15:30 - 16:30 Qiime2: Denoising. (Mariana Reyes)
16:30 - 17:30 Qiime2: Hands-on section. (Mariana Reyes)
Thursday, 04/07/2024
09:00 - 10:45 Qiime2: Taxonomic annotation and descriptive statistics. (Mariana Reyes)
Break
11:00 - 12:00 Qiime2: Alignment and phylogenetic reconstruction. (Mariana Reyes)
12:00 - 13:00 Qiime2: Qiime2: Hands-on section. (Mariana Reyes)
Break
14:30 - 16:00 Qiime2: Differential abundance analysis. (Mariana Reyes)
16:00 - 17:30 Qiime2: Qiime2: Hands-on section. (Mariana Reyes)
Friday, 05/07/2024
09:00 - 09:45 Creating scripts and pipelines. (Giuseppe D'Auria)
09:45 - 10:45 Students projects. (Giuseppe D'Auria)
11:00 - 12:00 NGS sequencing and beyond. (Rosario Gil)
12:00 - 13:00 Questionnaires and closure. (Giuseppe D'Auria)