The group for computational biology and bioinformatics at the Institute for Medical Genetics at the Charité offers challenging internships, bachelor and masterthesis for interested students of Computer Sciences and Bioinformatics.

Next Generation Sequencing

Sequencing techniques of the second generation are revolutionizing genetics. These high through-put techniques generate several orders of magnitude more sequencing data and challenge bioinformaticians. We use a Genome Analyzer II for genome wide mutation screening. We will sketch three projects, that could be dealt within the scope of a software engineering internship or Berufspraktikum of 8 weeks:

  • After a sequencing run the raw data consists of millions of short sequence reads that have to be aligned to a reference sequence before further analysis. After the alignment, one is interested how well the genomic region of interest is covered by short reads. The goal of this software internship is the development of a automatized pipeline, that computes the coverage of the target region an further meaningful statistics of a sequencing run.
  • NGS data sets as well as array CGH data sets generate a plethora of candidate mutation and copy number variation, that have to be validated using standard techniques. This requires the design of oligonucleotide primer sequences. The goal of this software internship is to further develop a pipeline, that generates for a given genomic position or interval the appropriate validation primer sequences.