NGI Stockholm (Genomics Applications Development)

National facility

NGI Stockholm (Production)

The Genomics Applications Development Facility offers state-of-the-art service in the rapidly developing field of massively parallel DNA sequencing.


  • Carry out user projects for applications not supported by the Genomics Production facility.
  • Establishing novel sequencing applications addressing the needs of users.
  • Outreach activities including provide guidelines and support for sample collections, study design and protocol selection.


  • The facility has full access to the instrumentation of the Genomics Production Facility.
  • 10X Chromium for long-range haplotyping and de novo assembly.
  • Oxford Nanopore MinION  for long-read sequencing (>10 kbp)


All of the applications below include a descriptive bioinformatic analysis (enquire for details). They are at different stages of initial testing, development and validation. If you are interested in something not on this list, please let us know! Please refer to the Genomics Production Facility page for the standard applications.

  • Low input and FFPE RNA seq and bioinformatic analysis. Includes RNA and/or DNA extraction.
  • Small RNA seq with bioinformatic analysis.
  • ChIP seq bioinformatic analysis (library prep in Genomics Production).
  • ATAC seq with bioinformatic analysis.
  • Bisulphite and oxidative bisulphite sequencing with bioinformatic analysis of whole human and non-model organism genomes.
  • Cancer Analysis Workflow for identification of somatic variants bioinformatic analysis (see pipeline).
  • 20 kb mate pair libraries for de novo genome sequencing and translocation identification
  • RAD seq (reduced representation sequencing) and bioinformatic analysis for population genetics with bioinformatic analysis.
  • User QC concept for low cost library preparation of microbial genomes (see tech note).
  • Exome and custom Agilent Sureselect capture (ISO accredited).
  • Custom sequence capture using Illumina and Roche/Nimblegen kits.


  • MultiQC: Summarize analysis results for multiple tools and samples in a single report.
  • Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression.
  • De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.
  • T-cell receptor-HLA-DRB1 associations suggest specific antigens in pulmonary sarcoidosis.
    • Grunewald J, Kaiser Y, Ostadkarampour M, Rivera NV, Vezzi F, Lötstedt B, Olsen RA, Sylwan L, Lundin S, Käller M, Sandalova T, Ahlgren KM, Wahlström J, Achour A, Ronninger M, Eklund A.
    • Eur Respir J. (2016) 47(3):898-909. doi: 10.1183/13993003.01209-2015 PMID: 26585430
  • The Norway spruce genome sequence and conifer genome evolution.
    • Nystedt B Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hällman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Käller M, Luthman J, Lysholm F, Niittylä T, Olson A, Rilakovic N, Ritland C, Rosselló JA, Sena J, Svensson T, Talavera-López C, Theißen G, Tuominen H, Vanneste K, Wu ZQ, Zhang B, Zerbe P, Arvestad L, Bhalerao R, Bohlmann J, Bousquet J, Garcia Gil R, Hvidsten TR, de Jong P, MacKay J, Morgante M, Ritland K, Sundberg B, Thompson SL, Van de Peer Y, Andersson B, Nilsson O, Ingvarsson PK, Lundeberg J, Jansson S.
    • Nature (2013) 497(7451):579-84. doi: 10.1038/nature12211 PMID: 23698360