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Next Generation Sequencing Core Facility (NGS-CF) in Freiburg

The Next Generation Sequencing Core Facility (NGS-CF) in Freiburg is a consortium of research laboratories at the Medical Center - University of Freiburg providing the technology and handling experience for any other Freiburg laboratory, wishing to perform their own next generation sequencing (NGS) reactions on site.

The institutions supporting this NGS-CF with their sequencing machines are the following:

  1. Center for Chronic Immunodeficiency (CCI) – Prof. Dr. Bodo Grimbacher
  2. Childrens Clinic – Prof. Dr. Charlotte Niemeyer, Dr. Marcin Wlodarski
  3. Department of Hematology and Oncology – Prof Dr. Justus Duyster, Dr. Cornelius Miething, Dr. Dietmar Pfeifer
  4. Institute of Clinical Pathology – Prof. Dr. Martin Werner, Prof. Dr. Silke Lassmann
  5. Institute for Human Genetics - Prof. Dr. Dr. Judith Fischer
  6. Institute for Infection Prevention and Hospital Epidemiology – Prof. Dr. Hajo Grundmann
  7. Institute for Transfusion Medicine and Gene Therapy (ITG) – Dr. Florian Emmerich, Prof. Dr. Toni Cathomen

While continuously expanding, NGS capabilities in Freiburg are still limited. Therefore, most NGS sequencing projects, especially the large-scale projects, will need to be outsourced. However, for specialized applications such as the sequencing of targeted gene panels, the sequencing of the microbiome, small-scale microbial population studies, small-scale library sequencing etc., our machines are equipped with sufficient sequencing power. Altogether, the NGS-CF at the Faculty for Medicine at the Medical Center - University of Freiburg currently possesses seven Illumina MiSeq NGS machines, each with a sequencing capacity up to 15Gb per run.

NGS-CF Nutzungsordnung



How to become a user of the NGS-CF?

Any researcher of the Faculty of Medicine in Freiburg may become a member or a user of the NGS-CF. Please apply for your password to access the MiSeq booking calendar at Prof. Dr. Bodo Grimbacher.

How to book a sequencing slot?

Typically, new users will identify a timeslot in our collaborative NGS booking calendar (www.cci.uni-freiburg.de/mrbs-1.4.8/web/day.php) to see which one of the NGS sequencers is available. They will then contact the respective person who is responsible for running this machine and its performance. The contact person will then train the newcomer on how to use the MiSeq and coordinate the sequencing process. Please be aware that some of the machines are used for clinical routine analysis, which has priority over experimental samples.

Who will prepare the NGS reactions?

Typically sequencing reactions are being prepared in the laboratory of the user, and also sequencing cartridges have to be bought by the respective user. Please verify with the NGS-CF which cartridges can be run on the MiSeq machine.

Who pays for the sequencing?

Each group will need to pay for its own reagents and sequencing costs. The NGS-CF only provides the MiSeq machine and is responsible for its maintenance and proper running.

How will I get my data out of the MiSeq?

Right now the MiSeq is not connected to the Network drive, so the user needs to copy the raw data to an external harddrive/ USB stick.

Will my data be stored?

The sequencing machine has only a small capacity to store data, therefore the data has to be deleted regularly.

Who will analyze my data?

Each user will have to analyze his/her data himself/herself. There is currently no bioinformatic service attached to the NGS-CF. However, we recommend to use the Galaxy platform provided by Prof. Dr. Rolf Backofen and Dr. Björn Grüning of the Technical Faculty Freiburg for NGS data analysis. Contact: https://galaxy.uni-freiburg.de

With respect to microbial whole genome analysis, interested people may contact Dr. Sandra Reuter at the Institute for Infection Prevention and Hospital Epidemiology.

For the sequencing of the microbial content in stool (human or mouse) please contact Katrin Hübscher from the CCI.


Prof. Dr. Bodo Grimbacher
+49 (0)761 270-77731