BIO326 Genome Sequencing; Tools and Analysis
Credits (ECTS):10
Course responsible:Matthew Peter Kent, Velma Tea Essi Aho
Campus / Online:Taught campus Ås
Teaching language:Engelsk
Limits of class size:20
Course frequency:Annually
Nominal workload:250 hours.
Teaching and exam period:This course starts in Spring parallel. This course has teaching/evaluation in Spring parallel.
About this course
Learning outcome
Knowledge
Each student should:
- be able to describe the principles behind nanopore DNA sequencing and explain the critical issues that can affect the success of a sequencing experiment, and assess raw data quality.
- be able to describe the use of and theory behind at least two specialized library preparation methodologies (e.g. HiC, ATAC).
- be able to clarify which processes must be performed to align DNA or RNA read data to a reference genome, identify SNPs, perform differential gene expression etc using the Galaxy infrastructure
- be able to critically assess literature and present an experimental plan for sequencing and assembling Prokaryotic genomes.
- be able to explain the key aspects behind metagenomic assembly and binning.
- demonstrate data sharing pipelines and describe the content and purpose of core online data repositories.
- be able to utilize what they have learnt to analyse a scientific question closely related to this courses content and contribute to discussion.
Skills
Each student should:
- Be able to perform end-to-end (sample to sequence) nanopore sequencing in the wet lab with limited support.
- Be able to login to Galaxy and Orion infrastructure and use appropriate bioinformatic tools for read alignment, genome assembly and annotation.
- Be able to critically assess the results from wet lab sequencing and dry lab bioinformatics and determine if they are suitable to answer the scientific question for which they were used.
- Be able to use R-studio for data visualization.
General competence
Each student should:
- Be able to analyse a scientific question related to what they have been taught and propose a strategy for answering it.
- Be able to communicate the results from wet or dry lab experiments to other scientists and to the general public.
- Be able to contribute to a Masters level project in terms of planning and experimental design, and selection of appropriate methodologies and analysis.
The course will involve lectures and group teaching as well as (wet and dry) lab work. Lectures, group discussions and practical bioinformatic exercises will be integrated to enable students to work on assigned tasks, which will include generating raw data, analyzing datasets and reporting their findings.
The wet-lab work is intended to give students practical experience with extracting DNA, assessing its quality, preparing it for sequencing (library production) and sequencing; the sequencing technology of choice will be long-read technology from Oxford Nanopore. Dry-lab work will entail running different bioinformatic software that are designed for genome assembly, binning, annotation and quality assessment. Students will work with both genome datasets from eukaryotes and prokaryotes as well as metagenomes from microbiome samples.
- Canvas
- Familiarity with a programming language (preferably Python and/or R), as well as a basic knowledge in molecular biology, microbiology and/or cell biology is required.
- Portefolio assessment: The examination is a combination of oral presentations and a project notebook that will follow the course’s experimental exercises and must be submitted 3 weeks after the course. The assessments will be marked as passed/not passed.
Portfolio Grading: Passed / Not Passed - The reports will be approved by an external examiner.
- Your presence and active participation in the entire course and in the group work are prerequisites for participating in the exam.
- Priority is given to students admitted to the Master program Genome Science (M-GS) because this is an obligatory course for them.
- Special requirements in Science. Students need to sign up at StudentWeb