Computational genomics (2015/2016)

Course code
4S003667
Name of lecturer
Nicola Vitulo
Coordinator
Nicola Vitulo
Number of ECTS credits allocated
6
Academic sector
BIO/18 - GENETICS
Language of instruction
English
Location
VERONA
Period
II semestre dal Mar 1, 2016 al Jun 10, 2016.

Lesson timetable

II semestre
Day Time Type Place Note
Monday 11:30 AM - 1:30 PM lesson Laboratory Alfa  
Friday 11:30 AM - 1:30 PM lesson Lecture Hall F  

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.

Syllabus

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.

Assessment methods and criteria

Written with open questions.

STUDENT MODULE EVALUATION - 2015/2016