BIO9905MERG1 - Bioinformatics for Metagenomic Analyses and Environmental Sequencing

Schedule, syllabus and examination date

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Course content

Metagenomics is the study of genomes recovered directly from environmental samples. This approach is often used to understand the genetic composition and metabolic capacity of microbial communities. Moreover, high throughput sequencing of amplified markers (DNA barcodes) can be used to analyse the taxonomic composition of environmental samples. In this course the students will be introduced to important analytical approaches used for analyzing microbial communities using high throughput sequencing.

Learning outcome

The student will be introduced to high throughput sequencing (methods and concepts) and how the data can be analyzed further to study microbial diversity and metagenomics. Important themes will be (1) filtering and quality assessment of high throughput sequence data, (2) clustering of high throughput sequence data, (3) taxonomic and genetic annotation of high throughput sequence data, (4) microbial diversity analyses, (5) analyses of microbial community composition and change and (6) metabolic reconstruction analyses. The main emphasis will be on the programs/bioinformatics pipelines Qiime and mothur.

Admission

PhD candidates from the University of Oslo should apply for classes and register for examinations through Studentweb.

If a course has limited intake capacity, priority will be given to PhD candidates who follow an individual education plan where this particular course is included. Some national researchers’ schools may have specific rules for ranking applicants for courses with limited intake capacity.

PhD candidates who have been admitted to another higher education institution must apply for a position as a visiting student within a given deadline.

Teaching

The course combines lectures (before lunch) and computer labs after lunch each day.

This is an intensive course over five days (March 27-31).

Examination

A project report will be compulsory and must be submitted two weeks after the course.
The report will be marked as passed/not passed.

Examination support material

No examination support material is allowed.

Grading scale

Grades are awarded on a pass/fail scale. Read more about the grading system.

Explanations and appeals

Special examination arrangements

Application form, deadline and requirements for special examination arrangements.

Evaluation

The course is subject to continuous evaluation. At regular intervals we also ask students to participate in a more comprehensive evaluation.

Facts about this course

Credits

5

Level

PhD

Teaching

Spring 2017

Examination

Spring 2017

Teaching language

English