Standardized Processing

Standardized Processing Service provides tried and test workflows and pipelines for omics data processing. All standardized processing services require well defined input data formats and data quality. Please contact us for further details.

Results from a Standardized Processing Service are usually made available in resources such as SODAR, VarFish, cBioportal, or SCelViz, for further self-service or third party downstream analysis.

Selected Standardized Processing Service

We continue to implement or retire services based on user needs and technological advances. Our current portfolio includes (but is not limited to):

Pipelines for Cancer Genomics

  • Exome Analysis (tumor/normal) including
    • data qc
    • alignment
    • SNV, Indel & CNV calling
    • rich variant annotation
  • Genome Analysis (tumor/normal) including rich variant annotation
    • data qc
    • alignment
    • SNV, Indel & CNV calling
    • rich variant annotation
  • Import in inhouse cBioportal instance for variant exploration
  • Neo-Epitope determination and binding prediction
  • MTC Trio (Exome & Transcriptome) with annotation

Further analysis, e.g. SV for WGS, single cell transcriptomics, etc. is available as Scientific Service

Pipelines for Rare Disease Genomics

  • Exome Analysis (index or trio)
    • data qc
    • alignment
    • SNV, Indel & CNV calling
    • rich variant annotation
  • Genome Analysis (index or trio)
    • data qc
    • alignment
    • SNV, Indel & CNV calling
    • rich variant annotation
  • Import in inhouse VarFish instance for variant exploration

Further analysis, e.g. SV for WGS, cohort or gene burden analysis, etc. is available as Scientific Service

Data Management

Includes but not limited to

  • VarFish import
  • cBioPortal import
  • SODAR import

Further solutions, e.g. SCelViz or Prodigy instance in KIOSC are available as Scientific Service

Functional Genomics

Our pipelines for (e.g.):

  • RNAseq analysis
  • Chipseq analysis
  • ATACseq analysis
  • Single Cell (10x) analysis

provide rich reports with qc, quantification, differential analysis, and enrichment statistics.

To achieve the best results, we always embed the corresponding processing in a small scientific service project.

Last modified: Jan 1, 0001