Welcome to the ODCF

The Omics IT and Data Management Core Facility (ODCF) provides high-throughput computing infrastructure, data management for sequencing and other research data and essential bioinformatic services to DKFZ groups and their collaborating partners.

ODCF Data Management

• Data Management Overview

  • Data Storage Structure – Information about the storage structure of sequencing and other research data at the ODCF
  • Project Setup – Instructions for setting up a new project at the ODCF
  • Project Member Management – Instructions on managing user access and roles within ODCF projects
  • Data Submission – Guidelines for registering sequencing data in OTP projects
  • External Data Submissions via ODCF GUIDE – Instructions for submitting external data via the ODCF GUIDE
  • Metadata Requirements – Explanation of metadata fields required for data submission into an OTP project
  • Sample Name Parser – Information on sample name parser in ODCF GUIDE to extract metadata from structured sample names
  • Data Withdrawal – Instructions for withdrawing samples and data from OTP projects

  Data Processing (OTP/Workflows)

  • ODCF Analyses – Overview of analyses provided by ODCF for sequencing data stored in OTP
    • Workflow Documentation – Bioinformatic workflows and quality overview
  • Single-Cell Data Processing with Cell Ranger – Instructions for processing single-cell RNA-seq data using Cell Ranger in OTP
  • IGV Linker - Instructions for accessing OTP workflow results via IGV Linker

  Data Sharing

  • Incoming Data Transfers – Instructions for importing external data into OTP projects via various methods
  • Outgoing Data Transfers – Instructions for transferring data from ODCF to collaborators
  • GHGA – Information on uploading data to the German Human Genome-Phenome Archive (GHGA)

ODCF IT Infrastructure

• DKFZ Compute Cluster

  • Compute Cluster – Information about the DKFZ Compute Cluster based on IBM LSF
  • Cluster Wiki – DKFZ cluster user documentation
  • Storage Offers – Information about the different storage options provided by ODCF
  • ODCF Transfer Server – Information on accessing the ODCF transfer server for external data transfers that cannot go through DKFZ proxy servers

ODCF Training

• ODCF Courses – Overview of the courses provided or co-led by ODCF members

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
• Positron - IDE with interactive data science tools for Python and R running locally on your device while using remote SSH connections to access the DKFZ cluster resources.
• Jupyterhub 01 - Jupyterhub 02 - Wiki - server for development and interactive analysis