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Hands-on short course on NGS analysis – from FASTQ to genotypes (2016)

ECTS credits: 2

Course parameters:
Language: English
Level of course: PhD cours
Time of year: Q1 2016
No. of contact hours/hours in total incl. preparation, assignment(s) or the like: 20 / 38
Capacity limits: 20 participants


Objectives of the course:
Students will become acquainted with the essential tools in the processing of whole genome sequence data all the way from raw, unfiltered FASTQ files to finished variant calls. All the intermediate steps will be introduced and at each step the students are familiarized with the required tools in hands-on practicals. Throughout focus is more on application than on the underlying theory.


Learning outcomes and competences:
At the end of the course, the student should be able to:

  • Identify and run the steps required in processing sequencing data
  • Explain what happens at each step and the reasons for including the step
  • Diagnose and solve errors arising during data processing
  • Reflect on computational efficiency of the pipeline
  • Interpret the results output by the data processing pipeline

Compulsory program:

  • Participation in lectures and exercises.
  • A project report on the activities during the exercises and an interpretation of the results obtained.

Course contents:


  • Filtering of FASTQ data
  • Alignment to a reference genome
  • Recalibration
  • Re-alignment of InDels
  • Variant calling
  • Variant annotation


  • Basic genetics and molecular biology
  • Basic skills in command-line use of Linux

Name of lecturers:

  • Pernille Sarup (course coordinator)
  • Bernt Guldbrandtsen

Type of course/teaching methods:
Four whole-afternoon sessions with a mixture of lectures/presentations and practical computer exercises analyzing real data. Writing a report based on the course exercises.


Course notes


Course homepage:


Course assessment:
Pass / not pass based on attendance of classes + approval of student report


Center for Quantitative Genetics and Genomics, Dept. of Molecular Biology and Genetics


Special comments on this course:
A laptop with PuTTY pre-installed and working access to Eduroam is required. No assistance is provided for this.


12 to 15 September, 2016 + assignment


Research Centre Foulum, Blichers Allé 20, 8830 Tjele


Deadline for registration is Monday, 29 August, 2016. Information regarding admission will be sent out no later than two days later.

For registration send an e-mail to


If you have any questions, please contact Pernille Sarup, e-mail: 

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Revised 05.11.2018