BMB838: Introduction to next generation DNA sequencing technology – methods and applications

Study Board of Science

Teaching language: Danish, but English if international students are enrolled
EKA: N210046102
Assessment: Second examiner: None
Grading: Pass/Fail
Offered in: Odense
Offered in: Spring
Level: Master

STADS ID (UVA): N210046101
ECTS value: 5

Date of Approval: 31-10-2022

Duration: 1 semester

Version: Archive


The course has limited entry. The following criterias are taken into consideration when seats are assigned.

1. Students with the most ECTS from their master
2. Students who are accepted conditionally on the master 
3. Students who follows master courses concurrent with their bachelor programme

If students are equal – seats are allocated based on random draw.
The academic envirometns at The faculty of science manages the prioritisation and at waiting list is established and will then be 
made aware from the faculty. The waiting list will not be transferred to the following year.

Entry requirements

Bachelor’s degree in Biomedicine, Biochemistry and Molecular Biology, Biology or Chemistry.

Academic preconditions

Students taking the course are expected to:

  • Have knowledge of the biochemical mechanisms regulating basic biological processes such as DNA replication and transcription.
  • Have knowledge of genome organization in prokaryotic and eukaryotic cells and understand the epigenetic mechanisms controlling genome organization.
  • Have knowledge of DNA sequencing technologies.  
  • Be able to use the most basic laboratory equipment such as micropipettes, centrifuges etc.
  • Be able to use the simple bash scripts and R for data analysis

Participant limit


Course introduction

The aim of the course is to enable the student to understand the basic principles of different types of next generation sequencing (NGS) technologies and provide extended theoretical and practical experience with Illumina based NGS. In addition, the course will provide the student with knowledge on the broad range of applications of NGS in basic science and the clinical.

The course builds on the knowledge acquired in the courses BMB508 and BMB822, and gives an academic basis for studying topics including genetics, epigenetics, genome organization, genome sequencing and gene regulation, that are all part of the degree.

In relation to the competence profile of the degree it is the explicit focus of the course to:
  • Give the competence to use NGS technology within life science ranging from microbiology to human biology.
  • Give a though introduction to the most used NGS technologies and an updated knowledge on upcoming DNA sequencing technologies. 
  • Give skills to sequence DNA using Illumina NGS based technology.
  • Give knowledge and understanding of the biochemical strategies to enrich the genomes and transcriptomes before sequencing.
  • Give knowledge and understanding of the advantages and disadvantages of the different types of NGS technologies used to sequence genomes, epigenomes, cistromes and transcriptiomes.

Expected learning outcome

The learning objectives of the course is that the student demonstrates the ability to:
  • Describe the basic principles for the most common NGS platforms such as Illumina, Iontorrent, Roche 454 and Pacific biosciences 
  • Explain the advantages and disadvantages with the different NGS platforms and describe which of the platforms would be most optimal to study the genome, epigenome and transcriptome. 
  • Explain the different steps of Illumina sequencing (DNA library synthesis, DNA sequencing and data analysis).
  • Describe different biochemical methods applied to enrich different parts of the genome and transcriptome before sequencing.
  • Synthesize and quality control DNA libraries for Illumina sequencing – synthesis, purification and multiplexing.
  • Understand and apply different types of quality control methods before, during and after Illumina DNA library synthesis.
  • Understand the output data files from Illumina sequencing and be able to perform the most basic NGS analysis (demultiplexing, genome alignment and DNA quantification). 
  • Use different types of NGS analysis tools. 


The following main topics are contained in the course:
  • The course material will include papers and reviews on topics covering the technological development of NGS and the different applications of NGS within life science including cell differentiation, cancer biology and microbiomics. In addition, the course will provide the student with the most updated protocols for synthesis of DNA libraries for Illumina based NGS. 
  • The theoretical part of the course will provide the student with a general understanding of different NGS platforms and upstream biochemical strategies to enrich the genome and transcriptome.
  • The practical part of the course will provide the students with in depth theoretical and practical knowledge on the synthesis of cDNA libraries from eukaryotic RNA and Illumina sequencing of the libraries (RNA-seq). This will include RNA purification, cDNA synthesis, adaptor ligation, DNA purification for Illumina sequencing.
  • After sequencing, the student will be introduced to the most basic bioinformatics strategies and will be provided with hands-on experience with demultiplexing, genome alignment, UCSC genome browser visualization and quantification of sequenced DNA fragments.     


See itslearning for syllabus lists and additional literature references.

Examination regulations

Exam element a)




Individual written report




Second examiner: None




Full name and SDU username


Normally, the same as teaching language

Examination aids

To be announced during the course 

ECTS value


Indicative number of lessons

70 hours per semester

Teaching Method

At the faculty of science, teaching is organized after the three-phase model ie. intro, training and study phase.

  • Intro phase (lectures) - 10 hours
  • Training phase: 60 hours, including 20 hours tutorials and 40 hours laboratory

The course is divided into lectures, paper presentations and a laboratory exercise. The lectures introduce the students to the recent NGS technology and application of NGS in research, the clinic and industry. The literature for these lectures is based on recent review papers. The lectures are followed by paper presentations by the student with primary focus on RNA-seq and ChIP-seq analysis. A subsequent laboratory exercise gives the student hands-on experience with the biochemistry used for DNA library construction for NGS and handling NGS technology. The student works in groups of 2-3 students under supervision of an instructor. The student starts by designing an experiment followed by RNA purification from mammalian cells, cDNA synthesis and NGS library construction. The student performs a series of quality control steps to ensure sufficient quality of the DNA libraries before sequencing. Following sequencing the student performs analysis of the RNA-seq data using publically available software (basic bash scripts and R). The student subsequently writes a paper on RNA-seq (from experimental design to quantification of RNA). The paper will be evaluated by an internal censor and graded as passed/fail.     

Studephase activities:

  • Student presentation of selected research papers
  • Analyse the quality control of NGS libraries
  • Analyse NGS data
  • Write a rapport on RNA-seq

Teacher responsible

Name E-mail Department
Lars Grøntved Institut for Biokemi og Molekylær Biologi


Administrative Unit

Biokemi og Molekylær Biologi

Team at Educational Law & Registration


Offered in


Recommended course of study

Profile Education Semester Offer period

Transition rules

Transitional arrangements describe how a course replaces another course when changes are made to the course of study. 
If a transitional arrangement has been made for a course, it will be stated in the list. 
See transitional arrangements for all courses at the Faculty of Science.