Software services (Galaxy etc.)

Galaxy is an open, web-based platform for data intensive biomedical research.
Try our VUmc-CCA Galaxy installation at:

http://galaxy.drylab.nl (reachable from outside VUmc, password protected)

Request an account from Christian (c.rausch AT vumc.nl). If you are new to Galaxy, please talk to Christian for an introduction on what you can do with Galaxy.

 

We currently have the following methods available. Please contact me if you are interested in applying these methods:

  • DNA copy number analysis from whole genome shallow (low coverage) sequencing using QDNAseq:
    • Method is fully automated with user-friendly web-interface on galaxy.drylab.nl
  • Variant Analysis from Amplicon sequencing data (Amplicon analysis pipeline AAP/Falco pipeline)
    • This method has been validated for a number of Cancer Genes with High Resolution Melting Curve assays and is currently used by Danielle Heideman for diagnostics.
    • Method is fully automated with user-friendly web-interface on galaxy.drylab.nl (currently in testing phase – become our first user!)
  • Differential Gene Expression analysis based on RNAseq data
    • 2 workflows available:
    • Analysis workflow developed by Irsan Kooi (PhD student with Josephine Dorsman and Jacqueline Cloos):
      • Partly available in in Galaxy: We would be happy to analyze your data and fully automate the workflow
    • A second workflow from Erasmus MC Rotterdam (Youri Hoogstrate / Prof Guido Jenster) is also available for comparison
  • Variant Analysis based on DNAseq: Targeted resequencing or Exome sequencing
    • Basic workflow is available in Galaxy on galaxy.drylab.nl, currently collaborating with Matias Mendeville (PhD student with Daphne de Jong and Bauke Ylstra) on benchmarking on FFPE samples