Learning outcomes

The advent of the new sequencing technology (Next Generation Sequencing, NGS), capable of producing million of DNA sequences in a single run at a relative low cost, had a great impact on the ability to study genome complexity at genomic, transcriptomic and epigenetic level and provided interesting opportunities for the development of bioinfomatic resources for data analyses and management.
The course will provide a general overview of the main computational methods that can be applied in genomic studies, mainly focused on the human genome. The course will include an overview on the main next generation sequencing technologies and several applications where these new technologies can be applied, as genome sequencing, genome resequencing for the identification of variants, transcriptomic analysis for the identification of differentially expressed genes.

Program

Introduction to next generation sequencing technologies (NGS)
Bioinformatics file format for data storage (FASTQ, BAM, VCF …)
Overview of genome assembly methods
Genome resequencing
Overview of NGS sequence alignment algorithms
identification of variants
identification of structural variation
Methods for variant prioritization and association to genetic disease
Transcriptomic analysis
Introduction to RNA-seq (sequencing the transcriptome with NGS)
RNA-seq alignment methods
Trascript reconstruction and quantification
Differential expression analysis

The course includes also practical exercise in the informatics laboratory about linux and bash, and analysis and management of NGS data.

Examination Methods

Written with open questions.