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Organizado por Alfredo García Fernández y Sergio Pérez Ortega

CV007 Introduction to Next-Generation Sequencing: Applications in Ecology and Evolution. IV Edition

  • Fechas:

    Del 01/07/19 al 05/07/19

  • Lugar:

    vicálvaro universidad rey juan carlos, Madrid, España (mapa)

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The course is aimed at graduates – postgraduates and PhD students on Evolutionary Biology and related sciences, interested in knowing the new tools and the potential that is being developed with the new techniques of massive parallel sequencing. Postdocs and senior researchers interested in apply NGS to new projects are also welcome. No specific training in bioinformatics is necessary.

The main objective of this course is to show a battery of potential applications of the NGS by researchers who are currently working with this technological approach. As an introductory course, the main purpose is not looking for a complex or deep training in a specific technique, but to give a broad view of the available approaches.

The assistant to this course should end with the feeling of knowing the techniques and their applications, with the purpose of being able to assess which ones may be interesting for their research or on which to deepen in later stages.


The specific objectives are:

1. To present an updated information on the different NGS techniques and their applications, potential and complexity.

2. To provide basic training in the main software for each of the techniques, as well as in data processing, and give tips on how to expand knowledge. This includes from the quality analysis, edition and analysis of the files to the interpretation of results. We aim that, with this basic knowledge, the student can be trained later if he is interested in a specific aspect of the ones addressed (for example, attending specialized courses or self-taught).

3. To favour the contact between students interested in specific techniques with teachers and specialized personnel, for possible collaborations or training.


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Course will be celebrate at room G-106 Edificio de Gestión.


Módulo I. Course presentation and introduction to Next Generation Sequencing techniques. Software installation and Linux environment.

10:00 - 11:00 Course presentation and students introduction. Alfredo Garcia ">11:00 – 11:30 Coffee break.

11:30 - 13:30 Introduction to NGS. Connection to virtual machine and software development. Alfredo García ">13:30 - 15:00 Lunch.

15:00 – 16:00 Introduction to Linux. Carlos Lara ">16:00 – 16:30 Break

16:30 – 18:30 Introduction to Linux. Carlos Lara ">Tuesday

Módulo II. First steps with NGS data: data editing and quality filtering. First pipelines in NGS. Dr. Alfredo García-Fernández  Dña. Sandra Sacristán. 

10:00 - 11:00 Some in Next Generation Sequencing. FastQ data. Alfredo García ">11:00 – 11:30 Coffee break.

11:30 - 13:30 Digging deeper. Edit and Data visualization. Data filtering. Carlos Lara ">13:30 - 15:00 Lunch.

Módulo III. Transcriptome, Gene Expresion and Gene Annotation Dña Sandra Sacristan y Drs. Alfredo García-Fernández y Carlos Lara Romero

15:00 – 16:00 Transcriptome analyses. Alfredo García ">16:00 – 16:30 Break.

16:30 – 18:30 Data assembly and alignment. Gene annotation. Sandra Sacristan ">Wednesday

Module IV. Locking for polymorphisms in the genome. RAD ">10:00 - 11:00. From the lab to the bioinfo. Differences between techniques. Applications to genomic studies. Hints and tips.

11:00 – 11:30 Coffee break.

11:30 - 13:30. Practical examples under supervision. Specific software to obtain SNPs and population studies.

13:30 - 15:00 Lunch.

Module V. Metagenomic and 16S. Dras. Andrea Meseguer y Maria Razzauti

15:00 – 16:00 Introduction to metagenomic approach, pro ">16:00 – 16:30 Break.

16:30 – 18:30 Practical examples under supervision. Specific software for metagenomics. R scripts in metagenomics.


Module VI – De Novo Assembly and Filogenetic Analyses José Carlos del Valle

10:00 - 11:00. Different approaches in NGS assembly. Is essential a reference genome? How perform phylogenetic and phylogeograhy analyses. Study cases and advice for your projects.

11:00 – 11:30 Coffee break.

11:30 - 13:30 Practical examples under supervisión. Software Geneious for aligment and assembly. Phylogenetic softwares: MrBayes, RaxML, etc.

13:30 - 15:00 Lunch.

Module VI. Evaluation of repetitive elements in the genome. Drs. Sònia Garcia, Vratislav Peska y Daniel Vitales

15:00 – 16:00 Introduction to theoretical concepts of repetitive elements of the genome. How to deal with a NGS project about repetitive element.

16:00 – 16:30 Break.

16:30 – 18:30 Practical session about repetitive elements. Specific software to repetitive elements analyses. Galaxy Server and Repeat explorer. Examples with Pisum sativum y Artemisia annua.



Module VII. Locking for polymorphisms in the genome (II). Genome capture approachs and SNPs. Dr. Santiago C. González-Martínez

10:00 - 11:00 Advanced research in NGS. Applications in conifers and trees.

11:00 – 11:30 Coffee break.

11:30 - 14:00 Final Lecture and Conclusions.

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