Welcome to the ODCF

The Omics IT and Data Management Core Facility (ODCF) provides high-throughput computing, data management for sequencing data as well as other research data and basic bioinformatics services to groups at the DKFZ and their collaborating partners.

• Data Management

  • Project Set Up – how to set up a project in OTP for sequencing or other research data
  • Data Storage – storage structure on the file system
  • Project & User Management – how to manage OTP project access rights
  • Data Submission – how to submit data via NGSCF or from external sources
  • Metadata Explanation – metadata stored in OTP
  • Sample Name Parser – possibility to parse information from the sample name into Guide metadata fields
  • Withdrawn Samples – samples no longer needed
  • Data Sharing – how to exchange data with collaborators
  • EGA – what is needed to upload your data to EGA

• Data Processing (OTP/Workflows)

  • Workflow Documentation – bioinformatics workflows and quality overview
  • Single Cell Data – cell ranger
  • ODCF Analyses – alignment, quality control and variant calling

• DKFZ Compute Cluster

  • Compute Cluster – computing platform based on IBM LSF
  • Cluster Wiki – DKFZ cluster user documentation
  • Storage Offers – where to store your data

• ODCF Software Tools / Webservices

  • ODCF Guide – tool for submitting and validating metadata for your submissions
  • One Touch Pipeline (OTP) - sequencing data and results GUI
  • IGV-Linker - genome visualization tool
  • RStudio Workbench - Wiki - server for development and interactive analysis
  • JupyterHub - Wiki - server for development and interactive analysis