Course code BIN310

BIN310 Selected topics in genome analysis

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Showing course contents for the educational year starting in 2019 .

Course responsible: Lars Gustav Snipen
ECTS credits: 10
Faculty: Faculty of Chemistry, Biotechnology and Food Science
Teaching language: EN, NO
(NO=norsk, EN=Engelsk)
Limits of class size:
50
Teaching exam periods:
This course starts in autumn parallel. This course has teaching/evaluation in autumn parallel.
Course frequency: Odd years
First time: 2006V
Course contents:
Modern sequencing technology, shotgun and amplicon sequencing. Assembly and annotations of genomes and metagenomes. Simulation of sequencing data, both Illumina and Nanopore. Analyses of data from microbial communities (readcount-tables).
Learning outcome:

KNOWLEDGE: The ideas behind commonly used algorithms for processing and analysis of sequence data. Get to know a UNIX computing cluster and simple shell scripting. Know some common statistical methods for metagenome-studies and apply these on real data using R and R-packages.

SKILLS: Be able to apply elements from the topics above to solve a project assignment in the course. Making simple shell-scripts and R-scripts and run heavier analyses on a UNIX computing cluster. Present material both orally and in a written report.

GENERAL COMPETENCE: Be able to make use of, and understand, the computational pipelines of the future. Practical programming competence, directed toward analysis og bio-data.

Learning activities:
Two lectures weekly. Two to four hours supervised solving of problems in the computer lab weekly. These classes can to some degree be used for ad-hoc lectures on topics of special interest, if requested by the students. Oral presentation of written report.
Teaching support:
Active use of Canvas.
Syllabus:
Will be specified at the beginning of the course.
Prerequisites:
Introduction to bioinformatics equivalent to BIN210. Statistics equivalent to STAT100.
Recommended prerequisites:
Programming and statistics beyond the introductory level. 
Mandatory activity:
A written report on a topic announced at the start of the course. Oral presentation of the report.
Assessment:
Written exam, 3.5 hrs, counts 100%
Nominal workload:
Lectures: 26 hours. Exercises with instructor present: 44 hours. Individual study: 230 hours.
Entrance requirements:
Special requirements in Science
Type of course:
Lectures: 2 hours per week. Computer lab exercises: 4 hours per week.
Note:
Students must bring their own laptop to computer-labs.
Examiner:
The exam will be approved by an external examiner. 25 selected exam papers will be evaluated by the external examiner.
Allowed examination aids: A1 No calculator, no other aids
Examination details: Written exam: Bestått / Ikke bestått