Processing & Visualization of NGS Data

In addition to storing raw data, we provide primary processing of various types of NGS data. Data registered in OTP is automatically processed using all available workflows. Currently we offer the alignment of human and mouse data. Our OTP supported workflows also include variant calling for tumor / normal sample pairs (SNVs, INDELs, CNVs, SVs), signature analysis, feature counts and other downstream analyses. All results are stored on the filesystem and also listed on the GUI. All processing steps are book kept to enable reproducibility. Additionally, sequencing coverage and quality checks are provided. The raw data and results are stored in a project-specific location so that the bioinformaticians can access the data and results directly.

Moreover, we offer the Heidelberg Unix Sequence Analysis Resources (HUSAR) program package which contains several workflows for NGS data and other tools to process sequencing data. It is a self-service system which can be used via a GUI or command line. Bioinformatic guidance may be provided in special cases. In case any further analyses are required, several different tools are provided on the HUSAR server and can be used.

The IGV Linker allows streaming of nearly all ODCF-managed data into your local IGV-session and can be accessed inside the DKFZ intranet. This is a visualization tool, which can replace the need for filesystem mounts or network drives. It provides a patient-based sorted view of the visualized data in your project and allows loading into IGV with a single click. After a one-time setup and fine-tuning, based on your project’s needs, the overview page is updated daily depicting the latest data from the filesystem.


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