Freerk van Dijk, ICT internship at GCC

As part of my bio-informatics course at the Hanze Hogeschool Groningen, I had to do an internship for 10 months. I did this in the Genetics Coordination Center (GCC) in the Department of Genetics, UMCG.

My research focused on setting up an analysis pipeline to detect disease causing variants from exome sequencing. To create this pipeline I used several open-source tools like BWA, Bowtie, VarScan and the Ensembl API. To retrieve additional information for biologists, I created a script which gathers information from OMIM and Genecards. Integrating these tools into one system resulted in the analysis pipeline for exome sequencing data.

At the start of my internship I had to learn a lot, because next-generation sequencing is a new and fast evolving field. This meant I had to understand how the different techniques work and get to know all the different data analysis tools. Because of the rapid changes in this field, it is a really challenging and interesting part of genetics. The GCC staff have a lot of knowledge about databases and accompanying models and structures. When I ran into problems there was always someone who had time to help me sort them out. In addition to this, doing my internship in the genetics department helped to increase my biological knowledge. Having daily contact with biologists combined with the ICT knowledge in the GCC made this internship a great learning experience.