INGLESE

Basic knowledge of genetics, molecular biology, evolution and population genetics.
Programming skills: bash scripting

Class lectures and practical computational lab activities, scientific articles reading and discussion, seminars

The course enables students to acquire advanced knowledge in genomic and in particular in genome assembly and whole genome data analyses, and to develop an understanding of the evolutionary processes underlying genomic diversity. In addition, computational skills will be acquired in bioinformatics applied to genomics.

The knowledge acquired will be applied in the understanding and analytical discussion of published studies and in the completion of laboratory activities.

Through the analysis and discussion of case studies and laboratory activities, students will acquire critical thinking autonomy, planning skills, and group work skills

What is genomics and which are the applications of genomics we will focus on during these course

Biodiversity Genomics initiatives (EBP, ERGA, Endemixit)

Genome structure and organization in viruses, bacteria, eukaryotes

Mutations as the source of genomic diversity

UNIX recap, Disva cluster connections, hands-on tutorials basic organization and workflow

Whole-genome resequencing data production and preparation: sequencing, raw reads quality filtering, genomic reads mapping, SNP calling and SNP filtering

Genomic data file formats: fastq, sam/bam, vcf

Whole genome assembly: challenges and golden standard pipelines. Long-read sequencing, optical mapping, chromatin contact maps, quality controls and preliminary analyses (k-mers), assembly (De Brujin graphs)

Genome functional annotation

Transcriptomics

Transposable Elements discovery, classification and annotation

The final examination consists of a written multiple-choice test and computer lab exercises
Exercises during lab activities
Presentations of scientific articles

Demonstration of having acquired the advanced knowledge proposed during the course, of being able to carry out the computer lab exercises, and of understanding and reporting on articles proposed during the course.

The final grade is awarded in thirtieths. The examination is deemed passed when the mark is greater than or equal to 18, the highest mark being 30 with honours.

The final grade is awarded on the basis of the outcome of the written test, supplemented by assessments of the exercises proposed during the course.

Introduction to Genomics, A. Lesk, Oxford University Press