Bioinformatics data analysis

Genomics data analysis

Our ‘Computing’ team is specialized in developing and maintaining automated computational (bioinformatics) pipelines for reproducible analyses of RNA or DNA Next Generation Sequencing (NGS) data. We offer routine pipelines with fast run times and consistent quality, but can also customize a suitable pipeline based on best practices, test it and run it for you, or install it wherever it is needed.

NGS techniques can sometimes also be arranged via us; we have a longstanding collaboration with the Genome Analysis Facility (NGS sequencing service facility) at our department.

Analysis software

We have several standardized pipelines based on combining individual software tools or modules and custom code and commercially available tools (GATK, Picard etc). To get an idea of the different pipelines that we offer, have a look at our pipelines section further below.

Before running or installing a new or updated pipeline, each component is tested with simulated and real data and the complete pipeline is validated before and after deployment on its final location.

Pipelines can be used on our system, by us. We can give access to the resulting data via an easy and secure data access procedure. We can also give access to a small part of our HPC environment where you can run the pipeline yourself, or in a cloud computing environment. If needed we install and deploy the pipeline locally, at your own servers, with pre-installed software that we deliver with the pipeline.

NGS bioinformatics pipelines

Below is a list of NGS sequencing data analysis pipelines that we currently offer:

demultiplexing
DNA analysis (wgs, exome, ssid, targeted panels)
RNA analysis (Lexogen, BiooScientific, Single Cell RNA seq data, ao)
Imputations
Custom pipelines

Bioinformatics in-house tools that we offer:

sorta mapping service
convading
gavin
molgenis compute

if you need more information, please contact Elisa Hoekstra (e.j.hoekstra at umcg.nl) or submit your request via the contact Form