Program Overview

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Program Overview

The University of Copenhagen offers a Master's program in Bioinformatics, which includes a course on Advanced Bioinformatics for Next-Generation Sequencing.

Course Description

The course covers advanced topics in Bioinformatics for analysis of data from next-generation sequencing (NGS). The course is based mostly on scientific papers and texts, and the topics include:

• Mapping algorithms
• Population genetic and medical genetic analysis based on NGS
• RNA-seq
• Cross-species comparative genomic analyses
• Other topics relating to high-throughput DNA sequencing

Learning Outcome

The student will know and understand the main methods used in the course. More specifically, the student will obtain knowledge of:

• Analysis of high-throughput sequencing data
• Genetic analyses
• Phylogenetic construction
• Genome evolutionary analyses

The student will be able to:

• Do the types of data analyses covered in the course
• Interpret results of such analyses in a biological context
• Explain the methods covered in the course
• Select the appropriate methods and tools for a given problem covered in the course

The student will obtain or improve these general competences:

• Will be able to discuss and explain methods in bioinformatics with researchers in bioinformatics and related sciences
• Will be able to contribute to interdisciplinary projects involving biological sequence analysis
• Will be able to read, understand, and discuss scientific literature in bioinformatics

Literature

The course literature is available on Absalon.

Recommended Academic Qualifications

Competencies corresponding to 3 out of 4 of the mandatory courses in the bioinformatics graduate programme or equivalent. Students must be on their second year. The course builds on several components that are taught in the first year, listed below, and is thus recommended for second-year students.

• Statistics
• Mapping and alignment, incl. Burrows-Wheeler transformation
• R programming for visualization and data manipulation
• Working with expression data (RNAseq)
• Experience with analysing short read NGS data
• Population genetics, pop structure, admixture
• PCA While it is of course possible to catch up by studying independently, the course may become rather challenging and time-consuming if all the expected qualifications are new to you.

Teaching and Learning Methods

The course consists of lectures and exercises (7 hours per week), and homework (4 in total).

Remarks

The course is identical to NBIK15022U Advanced Topics in Bioinformatics. It is not allowed to pass both courses. The course is prepared for the bioinformatics graduate programme, but it is open to third year BSc students and MSc students in general.

Workload

The workload for the course is as follows:

• Lectures: 40 hours
• Preparation: 122 hours
• Practical exercises: 24 hours
• Exam: 20 hours
• Total: 206 hours

Exam

The exam is a continuous assessment, with mandatory homework assignments. The grade is based on the average number of points obtained in the assignments. All aids are allowed.

Marking Scale

The marking scale is a 7-point grading scale, with no external censorship.

Re-exam

The re-exam is a renewed hand in of mandatory homework assignments.

Criteria for Exam Assessment

In order to obtain the grade 12, the student should convincingly and accurately demonstrate the knowledge, skills, and competences described under Learning Outcome.

Course Information

• Language: English
• Course code: NBIK20004U
• Credit: 7.5 ECTS
• Level: Full Degree Master
• Duration: 1 block
• Placement: Block 1
• Schedule: C

Study Board

The study board for the course is the Study Board for the Biological Area.

Contracting Departments

The contracting departments for the course are the Department of Biology and the GLOBE Institute.

Contracting Faculty

The contracting faculty for the course is the Faculty of Science.

Course Coordinators

The course coordinator for the course is Anders Albrechtsen.