National Genomics Infrastructure – Stockholm

NGI Stockholm consists of two groups; Genomics Production and Genomics Applications Development, and offers state-of-the-art service in the rapidly developing field of massively parallel DNA sequencing.  Genomics Production offers library preparation and high-throughput sequencing followed by data processing and best practice analysis for a variety of well established applications. Genomics Production is Swedac accredited, which ensure that projects are completed in accordance with rigorous quality standards. Genomics Applications Development collaborates with researchers on applications not supported by Genomics Production, for more information see application list below.

Services

• DNA and RNA sequencing of user provided samples
• Establishing novel sequencing applications addressing the needs of users
• Outreach activities including provide guidelines and support for sample collections, study design and protocol selection

For a full list of the services that we offer, please see our website: https://ngisweden.scilifelab.se/applications/

Applications

These standard applications are currently performed by the Genomics Production and are ISO accredited:

• Human whole-genome sequencing with best-practice bioinformatic analysis (see details)
• Non-human whole-genome sequencing
• Strand-specific RNA sequencing (RNA-seq) with best-practice bioinformatic analysis for supported genomes (see details)
• Small RNA sequencing with bioinformatic analysis. See Tech Note. Low input by GAD.
• De novo genome sequencing with best-practice bioinformatic analysis including 3-5 assemblies (see details). Multi-library assembly by GAD.
• Metagenomics
• Sequencing of finished library

The following applications are handled by the Genomics Applications Development and are at different stages of initial testing, development and validation. These applications usually include a descriptive bioinformatic analysis (enquire for details). If you are interested in something not on this list, please let us know!

• Low input and FFPE RNA seq and bioinformatic analysis. Includes RNA and/or DNA extraction
• Low input smRNAseq and bioinformatic analysis. Includes RNA and/or DNA extraction
• ChIP seq bioinformatic analysis (see Tech Note)
• ATAC seq with bioinformatic analysis
• HiC for de-novo genome scaffolding and epigenetics studies
• Bisulphite and oxidative bisulphite sequencing with bioinformatic analysis of whole human and non-model organism genomes
• Sarek 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
• De-novo multi-library assembly bioinformatic analysis
• 16S and custom amplicon automated library preparation and sequencing
• User QC concept for low cost library preparation of microbial genomes (see tech note)
• Library preparation automation for large projects. See our Bravo protocol scripts on GitHub
• Automation of large-scale bioinformatic analyses such as RNA-seq, smRNA-seq, ChIP-seq and Methyl-seq
• Software development for quality control (MultiQC) and running small pipelines (Cluster Flow)

Equipment

• Illumina NovaSeq
• Illumina MiSeq for sequencing of small genomes and amplicons
• Illumina cBot
• Agilent Bravo
• Agilent NGS Workstation
• Agilent Bioanalyzer
• Tecan Infinite 200 PRO
• Caliper LabChip XT
• Caliper LabChip GX
• Bio-Rad CFX
• Covaris
• Fragment Analyzer
• Oxford Nanopore MinION  for long-read sequencing (>10 kbp)

Using the facility

For any other inquiries, including specific questions about the services, please e-mail NGI Stockholm at support@ngisweden.se