NGS bioinformatics

The NGS Bioinformatics Unit is an infrastructure service unit part of the HiLIFE (Helsinki Institute of Life Science), UH (University of Helsinki), and FIMM (Institute for Molecular Medicine Finland) organizations.

We provide assistance in the experimental design of next generation sequencing (NGS) experiments, support for the analysis of model organism related NGS data, and have mature best-practice and computational solutions for a variety of model organism related NGS applications. Please note that sequencing analyses acquired from the FIMM sequencing unit include our basic services.

Services:

  • RNA-seq data analysis (basic)
  • miRNA-seq data analysis (basic)
  • Detection of germline variants (basic / advanced)
  • Somatic variant discovery
  • Copy-number alternation analysis
  • Variant filtering and annotation
  • Association testing between rare variants and phenotypes
  • Differential gene and allele-specific expression analysis

User fees:

Price estimates for University of Helsinki customers given below (VAT 0%). The final price of the service may vary based on size and complexity. To request a quote, please contact the unit.

Sequencing done at the FIMM sequencing unit include basic services

Provided analysis External NGS data

Re-analysis

 FIMM sequencing
RNA-seq data-analysis (basic) 300 35 0
miRNA-seq data-analysis (basic) 150 10 0
Germline variant calling (basic) 150-300 25-75 0
Germline variant calling (advanced) 300 150 150
Somatic variant calling (advanced) 300 150 150
Variant filtering and annotation 50 25 25
Copy number alteration 150-250 35-75 75-125
Differential expression analysis >1000 >1000 >1000
Association test >1000 >1000 >1000

User access policy:

Open access service where customer prioritization is done as first-come, first-serve basis.

User guidelines:

Analyses are performed in the order of arrival / requests

Turnaround time of best practices is about 3 days per sample, but may vary based on the size and complexity of the data

Contact person:

Team leader Matti Kankainen, matti.kankainen@helsinki.fi

Location:

Biomedicum Helsinki 2, Tukholmankatu 8, Meilahti campus, Helsinki