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core-unit-bioinformatics

Core Unit Bioinformatics

Welcome to the GitHub profile of the Core Unit Bioinformatics (CUBI) of the Medical Faculty and University Hospital of the Heinrich Heine University Düsseldorf (Germany).

Our mission

The CUBI offers bioinformatic expertise and analysis support for all researchers at the HHU. We are your scientific partners, starting from initial project counseling, to data clean-up, reproducible data processing and in-depth evaluation of the results. The service catalog of the CUBI builds on the work of the global bioinformatics and open source community. We do our part in giving back to the community by writing clean and reusable analysis workflows that are publicly available under a permissive license and deployable in standardized ways.

Our services

(The CUBI service catalog is currently being compiled)

Our references

Please take a look at the list of published research projects supported by the CUBI.

Contact us

For specific feedback (bug reports, questions or suggestions) to any of our repositories, please open a GitHub issue in the respective repository.

If you want to get in touch, you can reach us at:

core [dash] unit [dash] bioinformatics [at]
med [dot] uni [dash] duesseldorf [dot] de

The (German) institutional website of the CUBI is hosted at the HHU/UKD.

Our team

Core members

Dr. Peter Ebert

Dr. Peter Ebert

Core Facility Manager

Affiliations:

  1. Core Unit Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
    • Postal address: Moorenstr. 5, 40225, Düsseldorf, Germany
  2. Center for Digital Medicine, Heinrich Heine University Düsseldorf, Germany
    • Postal address: Moorenstr. 5, 40225, Düsseldorf, Germany

Dr. Mirela Bălan

Dr. Mirela Bălan

CUBI staff scientst

Affiliations:

  1. Core Unit Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
  2. Center for Digital Medicine, Heinrich Heine University Düsseldorf, Germany

Associated members

Kai Horny

Dr. Kai Horny

Staff scientist via ZPM

Affiliations:

  1. Center for Personalized Medicine Oncology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
    • Postal address: Moorenstr. 5, 40225, Düsseldorf, Germany
  2. Core Unit Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany

Dr. Sven Willger

Dr. Sven Willger

Staff scientist via MODS

Affiliations:

  1. Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
    • Postal address: Moorenstr. 5, 40225, Düsseldorf, Germany
  2. Center for Digital Medicine, Heinrich Heine University Düsseldorf, Germany
  3. Core Unit Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany

Students

Aliz Fodor

Aliz Fodor

Student assistant / codet

Former members

sven_berres

Sven Berres

Staff scientist in 2023

Pinned Loading

  1. knowledge-base knowledge-base Public

    The CUBI's public knowledge base: a Wiki for how-to instructions, best practices and helpful hints

    1

Repositories

Showing 10 of 20 repositories
  • workflow-smk-sequence-annotation Public

    Snakemake workflow to annotate genomic sequences

    core-unit-bioinformatics/workflow-smk-sequence-annotation’s past year of commit activity
    0 MIT 0 0 0 Updated Mar 9, 2025
  • workflow-smk-longread-variant-calling Public

    Snakemake workflow for genome variant calling using long reads

    core-unit-bioinformatics/workflow-smk-longread-variant-calling’s past year of commit activity
    1 MIT 0 0 0 Updated Mar 6, 2025
  • cubi-tools Public
    core-unit-bioinformatics/cubi-tools’s past year of commit activity
    Python 0 MIT 0 5 1 Updated Feb 18, 2025
  • core-unit-bioinformatics/workflow-smk-genome-hybrid-assembly’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Feb 12, 2025
  • workflow-smk-assembly-evaluation Public

    Workflow for (vertebrate) assembly evaluation

    core-unit-bioinformatics/workflow-smk-assembly-evaluation’s past year of commit activity
    0 MIT 0 3 0 Updated Feb 12, 2025
  • project-run-hgsvc-hybrid-assemblies Public

    Project repository for the HGSVC phase 3 paper

    core-unit-bioinformatics/project-run-hgsvc-hybrid-assemblies’s past year of commit activity
    Shell 0 MIT 0 0 0 Updated Feb 12, 2025
  • template-snakemake Public

    Workflow template for Snakemake

    core-unit-bioinformatics/template-snakemake’s past year of commit activity
    Python 0 MIT 1 15 0 Updated Feb 5, 2025
  • template-metadata-files Public

    Collection of metadata files (gitignore, pyproject, editorconfig, license etc.) to be used for initializing workflow and project repositories

    core-unit-bioinformatics/template-metadata-files’s past year of commit activity
    0 MIT 0 0 0 Updated Jan 27, 2025
  • knowledge-base Public

    The CUBI's public knowledge base: a Wiki for how-to instructions, best practices and helpful hints

    core-unit-bioinformatics/knowledge-base’s past year of commit activity
    1 MIT 0 0 0 Updated Jan 17, 2025
  • workflow-smk-genome-onesie-assembly Public

    Snakemake workflow to create genome assemblies using only a single long-read sequencing technology (no hybrid assembly)

    core-unit-bioinformatics/workflow-smk-genome-onesie-assembly’s past year of commit activity
    0 MIT 0 0 0 Updated Jan 16, 2025

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