NGS and Bioinformatics

The Agency's Next Generation Sequencing (NGS) platform performs massive parallel sequencing of DNA and RNA. The platform is part of the Agency's preparedness platform but also offers analyses performed by the Agency's diagnostics service. The platform was established in 2012 and is currently used as a primary epidemiological typing tool for a number of different agents.

NGS and Bioinformatics Training 2023

The Public Health Agency offers training in NGS and Bioinformatics. These trainings are primary aimed for clinical microbiology laboratories who want to implement NGS technology and data analyses in their operations.

Upon request, the Public Health Agency can offer customized courses in NGS and Bioinformatics. Please send an e-mail for more information and price.

Customer support

Department of Microbiology offers customer support on a daily basis. For questions regarding for example our analyses, sampling, expert advice you can contact us either by phone, weekdays 9.00–12.00 and 13.00-15.30, or E-mail.

Phone: +46-10-205 24 44

E-mail to Customer support

NGS analyses

A number of different NGS-based analyses are offered by the Agency's special diagnostics service.

Whole genome sequencing of bacterial isolates

Whole genome sequencing (WGS) of bacterial isolates is offered for contact tracing or issues of antibiotic resistance.

Whole genome sequencing of SARS-CoV-2

WGS of SARS-CoV-2 is offered for contact tracing or other issues.

16S metagenomic sequencing

16S sequencing is carried out to determine which bacterial species are present in a clinical sample or isolate. The platform's method involves deep sequencing two fragment of the 16S rRNA gene, with an automated method being used to analyse data. The result is a list of database hits and an estimated quantity compared with an internal standard.

Metagenomics for detection of an unknown pathogen

Metagenomic sequencing is offered in cases where infection is suspected but other methods have failed to identify a pathogen. All nucleic acid in the clinical sample is sequenced and data is analysed by a bioinformatician. The result is a technical report, a list of database hits and an interpretation of potential clinical relevance following consultation with a clinical microbiologist.

NGS bioinformatics

The NGS platform analyse sequencing data and develop software that is used by our microbiological operation. Two of these software products are available externally to customers.


Software to continually monitor recently published sequences in order to detect mutations that may affect the sensitivity of PCR-based diagnostics. By adding primer systems to the Agency's database, it is possible as an external customer to have them continually monitored and to have potential problems reported by e-mail.


Software for designing primers and probes for PCR-based methods.

Customer support

If you are interested in our services please contact our customer support, see under Customer support.

For our contract customers, for referral of diagnostic samples please contact customer support during office hours (weekdays 09.00–12.00, 13:00-15:30 CET) or after office hours our clinical microbiologist on duty on +46-10-205 24 00.

NGS and Bioinformatics Training 2023

The Public Health Authority offers training on request in NGS and bioinformatics. These trainings are aimed at clinical microbiology laboratories who want to implement NGS technology in their operations.

  • Microbiological NGS workflow and data processing, on request.
  • Microbiological Bioinformatics, on request.