Introduction

• General overview of the course.
• NGS technologies vs. analysis methods and webtools.

Presentation.

• Basics of the NGS technologies.
• Computing infrastructure for NGS analyses.
• Some remarks on experiment design.

• NGS data preprocessing. Handling sequence files. Quality control tools.NGS data preprocessing
• Mapping. Reference genome as a concept. NGS alignment programs and algorithms. SAM/BAM and BED file formats overview. Mapped reads visualization. Quality control of the mapping. Local realignment. Computational needs.MappingVisualization
• Variant Calling. Variant types: SNPs and InDels. Calling procedures and algorithms. VCF file formats overview. Introduction to the programs GATK, Annovar and Variant. Variant filtering. The problem of the missing data. Variant annotation. Data bases and data repositories: dbSNP, the 1000 Genomes Project and CIBERER Spanish Variant Server.Variant Calling

Will be held in the cafeteria of the CIPF.

Web tools to analyze omic data.

• BiERapp. Interactive web application for assisting in gene prioritization in Whole-Exome Sequencing studies. (Presentation).
• CSVS (CIBERER Spanish Variant Server). This database provides information about the variability of the Spanish population. It is very useful for filtering polymorphisms and local variations when prioritizing candidate disease genes. CSVS
• Genome Maps. A modern and high-performance web-based HTML5 genome browser. Presentation

• TEAM (Targeted Enrichment Analysis and Management):
  • Management of panels of genes for targeted enrichment and massive sequencing for diagnostic applications.
  • How to design panels of genes.TEAM
• Cell Maps. An open-source web-based HTML5 systems biology tool for visualizing and analyzing biological networks. https://github.com/opencb/cell-maps/wiki

• Introduction to Babelomics 5. Babelomics Intro.
• Preprocessing, Differential Expression and Functional Profiling. Babelomics: RNA-Seq.
• Hands on.

Will be held in the cafeteria of the CIPF.

• Working with all analysis webtools. Bring your data!
• Babelomics: hands on.
• http://www.ngscourse.org/

• NGS data preprocessing, mapping and variant calling. Bring your data!

Functional profiling and detection of new functional candidates:

• SNOW. Network Enrichment.
• Network Miner. Gene Set Network Enrichment.
• network_analysis_from_babelomics5.pdf

• Introduction: signal transduction
• Signaling Pathways Analysis
• Presentación pathways
• Práctica pathways
• http://bioinfo.cipf.es/apps-beta/ciberer-course-data/pathways_data.zip

Will be held in the cafeteria of the CIPF.

• Babelomics 5.0: functional interpretation for new generations of genomic data. Alonso R, Salavert F, Garcia-Garcia F, et al. Nucleic Acids Res. 2015;43:W117-W121.
• Assessing the impact of mutations found in next generation sequencing data over human signaling pathways. Hernansaiz-Ballesteros RD, Salavert F, Sebastián-León P, Alemán A, Medina I, Dopazo J. Nucleic Acids Res. 2015;43:W270-W275.
• Understanding disease mechanisms with models of signaling pathway activities. Sebastian-Leon P, Vidal E, Minguez P, et al. BMC Syst Biol. 2014;8(1):121.
• Inferring the functional effect of gene expression changes in signaling pathways. Sebastián-León P, Carbonell J, Salavert F, Sanchez R, Medina I, Dopazo J. Nucleic Acids Res. 2013;41:W213-W217.
• A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. Alemán A, Garcia-Garcia F, Salavert F, Medina I, Dopazo J. Nucleic Acids Res. 2014;42:W88-W93.
• A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications. Alemán A, Garcia-Garcia F, Medina I, Dopazo J. Nucleic Acids Res. 2014;42:W83-W87.
• SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Minguez P, Gotz S, Montaner D, Al-Shahrour F, Dopazo J. Nucl. Acids Res. 2009;37:W109-114
• Genome Maps, a new generation genome browser. Medina I, Salavert F, Sanchez R, et al. Nucleic Acids Res. 2013;41:W41-W46.

• More publications.
• Computational Genomics tools