Subject description for 2019/2020

High throughput sequencing of non-model organisms (DR425F)

High throughput sequencing of non-model organisms

DR425F

Course description

Course content: Introduction to next-generation sequencing (NGS), Practical module: Prepare and run fragment library on the Illumina NextSeq, Bioinformatics: Basic computational resources and skills needed for HTS; mapping and query of NGS data, Sampling representative genomic sequence data from non-model species; Reduced Representation Libraries (RRL) and Restriction site Associated DNA (RAD) sequencing; enriching specific genomic targets for resequencing, RNA-Seq, transcriptomics, and non-coding RNAs, miRNAs and small RNAs of non-model species, Population genomic approaches, Current developments in NGS, Participants' presentations of own projects

 

Costs


Tuition fee 2 500 NOK. Lodging is available for students not affiliated with Nord University (contact Truls Moum). Students will have the option to analyze their own samples during the course, at the expense of some of the materials used (contact Truls Moum for further information). Other course materials and sundry expenses will be covered.


Learning outcomes

On successful completion of the course the student should have the following learning outcomes

Knowledge
The student should:
- have a general understanding of the power and limitations of high-throughput sequencing technologies
- understand the specific strengths and weaknesses of alternative high-throughput sequencing approaches
- understand the principles of de novo genome and transcriptome assembly
- understand how to assess transcript prevalence from RNA-seq data

Skills
The student should:
- be able to prepare a genomic library and perform a sequencing run at a NGS platform
- be able to make use of basic computational resources for NGS
- know how to transfer large data sets between computers
- be able to execute scripts and run extended analyses
- be able to map short-read sequence data to sequenced genomes and query the mapping for variation

General competence
The student should:
- be able to address biological questions in non-model species using short sequence reads
- be able to choose the most suitable sequencing technologies and analytical tools to be used to address the problem at hand
- be able to convey essential topics, exchange experiences, and keep updated within the field of high-throughput sequencing

Course type

Elective: PhD Aquatic Biosciences

Prerequisites

All PhD students at Faculty of Biosciences and Aquaculture, Nord University, and PhD students unaffiliated with Nord University are eligible. An application is required by April 10, 2017. We acept a maximum of 10 students; students unaffiliated with Nord University will be admitted on a first come, first served basis.

An application form can be found by following this link: http://www.nord.no/en/news-events/calender/Pages/PhD-course-High-throughput-sequencing-of-non-model-organisms.aspx

Mode of delivery

Face-to-face teaching.

Teaching activities and methods

Lectures, lab exercises, individual presentations, and feedback.

Recommended prior knowledge

Basic computer skills and some knowledge of molecular biology and genomics.

Course evaluation

Evaluation questionnaire to be provided to the students at the end of the course.

Assessment and examinations

Written assignement, grading scale Bestått - Ikke bestått
  • Oral presentation, grading scale Bestått - Ikke bestått.

Course literature

The reading list can be found in Leganto
Course coordinator
Start semester Spring 2020 ECTS Credits 5 Course location Bodø Faculty
Faculty of Biosciences and Aquaculture