The Bioinformatics Core of the University Medical Center Hamburg-Eppendorf (UKE) offers a wide range of bioinformatics services. The main focus is on the analysis of high-throughput sequencing data. Services offered include data analysis, consulting, software development, and training.

Services are usually offered free of charge and they geared primarily to researchers at the UKE and the University of Hamburg. The facility is, however, also open for collaborations with external partners.

Data Analysis

For many data analysis tasks standardized workflows, following published best-practices, are established at the Bioinformatics Core. For solving tasks were these workflows do not suffice, customized and integrative solutions are provided. In both cases the facility operates with a high degree of transparency, explaining and documenting analysis strategies and assessing results jointly with clients.

An incomplete list of often regularly conducted data analysis tasks:

  • Transcriptome Analyses (single-cell and bulk RNA-seq)
    • Differential Expression
    • Aberrant Expression
    • Aberrant Splicing
    • Fusion Genes
    • Monoallelic Expression
  • Germline and Somatic Variant Calling
    • SNVs, Indels
    • Structural Variants
    • CNVs
  • Metagenomics- and Metatranscriptomics-Analyses
    • WGS, rRNA/Marker Genes
    • Detection of Pathogens
  • Gene Set Enrichment and Overrepresentation Analyses
  • Genome and Transcriptome Assembly
  • Ribo-Seq
  • MeDIP-Seq
  • Bisulfite Sequencing
  • Various Data Annotation Tasks
  • Integrative Analyses


The facility provides consulting on various aspects of bioinformatics, sequencing and sequence data analysis. Many research projects are supported over their whole live cycle. This includes initial project planning, official support for grant applications and documentation of applied methods for publications.
Additionally the Bioinformatics Core gives advice on hardware and software solutions for workgroups who plan to carry out some or all analyzes by themselves.

Software Development

The Bioinformatics Core has substantial expertise in developing custom software and workflows for sequence data analysis. Software development, however, is often a time consuming process and thus the facility is forced to carefully evaluate the feasibility of proposed projects.


We are an official training partner within the German Network for Bioinformatics Infrastructure (de.NBI) and offer hands-on training courses focused on bioinformatics and computational biology. Training activities aim at enabling life scientists to effectively handle and interpret biological data.

Register for our upcoming training events here.