Course code BIN310

BIN310 Selected topics in genome analysis

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Showing course contents for the educational year starting in 2015 .

Course responsible: Lars Gustav Snipen
Teachers: Lars Gustav Snipen, Niklas Mähler
ECTS credits: 10
Faculty: Department of Chemistry, Biotechnology and Food Science
Teaching language: EN, NO
(NO=norsk, EN=Engelsk)
Limits of class size:
Maximum 100
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 shotgunand amplicon sequencing. Assmbly of genomes, RNAseq data and metagenomes. Sequence-variants (SNP-detection, orthologs, genotyping). Analyses based on whole-genome data. Metagenome studies and analyses of microbial communities. Even if most of the topics are related to microbiology most methods will have a more general nature.
Learning outcome:

KNOWLEDGE: Use of various sequencing technologies and know how we can get from reads to more informative sequences. Be able to sketch a selection of assembly algorithms. Have a good theoretical understanding of comparison and classification of sequences. Know some common statistical methods for association studies and use these on real data.

SKILLS: Students will be able to: Apply elements from the topics above to solve a project assignment in the course. Implementing the algorithms in R and use this scripting language for effective processing of large data sets. Present material both orally and in a written report.

Learning activities:
Two lectures weekly. Two to four hours supervised solving of problems in the computer lab weekly. These hours can also 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 Fronter.
Syllabus:
Will be specified at the beginning of the course.
Prerequisites:
Introduction to bioinformatics equivalent to BIN210. Programming knowledge equivalent to INF120. Statistics equivalent to STAT200/STAT210.
Recommended prerequisites:
Statistics equivalent to STAT300 or STAT310.
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 radomly selected exam papers will be evaluated by the external examiner.
Allowed examination aids: No calculator, no other aids
Examination details: Written exam: A - E / Ikke bestått