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Unix / UPPMAX & Next generation sequencing / genome analysis

The course is divided into two parts, where Part I (Unix / UPPMAX) is optional. Note that you are required to have the equivalent knowledge and experience corresponding to Part I of the course in order to be accepted to Part II (Next generation sequencing / genome analysis). If you don’t have the equivalent knowledge and experience, we strongly recommend you to attend Part I before starting Part II. Please consider the “test” in the application form if you are uncertain about what skills that are needed.

Part I

Unix / UPPMAX (1 hp)

2013-04-11– 2013-04-12

Linux / UPPMAX

The course will include basic concepts and commands used in Linux. When the course is over, the students are expected to know how to navigate the file system, how to read and edit files, create folders and move files, and understand how to manage their files. The course will also five an introduction to high-performance computing and large scale storage for bioinformatics, using the UPPNEX resources at UPPMAX. The course starts with describing the architecture of UPPMAX and gives hands-on experience with working with data and different types of storage. The next part describes how to work with UPPMAX interactively, and continues with explaining the job queueing system with tutorials on how to submit and monitor jobs. The last part is a hands-on tutorial where students gets to try a few software on UPPNEX for analyzing sequence data.

Entry requirements

A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable is desirable

Responsible teachers

Martin Dahlö, Ola Spjuth

Part II

Next generation sequencing / genome analysis (1.5 hp)

2013-04-15 – 2013-04-19

This course will provide an introduction to a wide range of analytical techniques for massively parallel sequencing. We will pair lectures on the theory of analysis algorithms with practical computational exercises demonstrating the use of common tools for analyzing data from each of several common sequencing study designs.

Entry requirements:

  • A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable is desirable.
  • The Linux / UPPMAX course or equivalent knowledge and experience.

To get the maximum benefit from the course we would like you to have

  • Relevant previous experience in sequencing or analysis
  • A current research project where you are currently using next generation sequencing or are planning to use next generation sequencing.
  • It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others.

Selction criteria

Correct entry requirements, motivation to attend the course as well as gender and geographical balance.
Responsible teachers: Manfred Grabherr, Lisa Klasson

Course information

National Course. The course is open for PhD students, postdocs, researchers, and other employees in need of bioinformatic skills within all Swedish universities

Important dates:

March 11th
Application deadline

March 12th 
You will receive a confirmation that we have received your application.

March 15th
You will receive an email stating that you have been accepted to the course or an email stating that you have not been accepted to the course

If you don’t receive information according to the dates above, contact:

Course fee

A course fee of 2500 SEK (1800 SEK if you don’t apply to the Unix/UPPMAX part) will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinner).