Summer schedule for placing orders and delivery of samples 2019 (2019-06-05)

We inform our users that NGI-Stockholm and NGI-Uppsala (UGC and SNP&SEQ) will work at a reduced pace during the summer 2019 and therefore we notify that:

  • Last day for placing orders at our order portal (to be processed before the summer) is June 18th.

  • Last day for sample delivery is June 28th.

New and old users are most welcome to place orders from August 6th. Happy summer!!

We're hiring! (2019-03-19)

We are looking for a research engineer for our production team to work with library preparations and quality controls. We are looking for someone who is very careful and responsible and thrives on daily handling and preparation of important samples in a quality-assured laboratory environment to promote research throughout Sweden. The samples are varied and the methods advanced, so some problem solving is a natural part of the work.

Read more about the job here.

NGI and NBIS provide drop in consultation meetings for those preparing VR applications (2019-03-05)

Welcome to a free drop-in session to discuss your plans and study design with us at your local university before submitting your VR application!

Meet our bioinformatics experts and sequencing coordinators to discuss new technology updates, input on your study design, opportunities for bioinformatics support, and guidance on the new data management plans.

Find schedule and more information here.

Season's greetings from NGI! (2018-12-21)

In the upcoming months NGI is planning to phase out both the HiSeq 2500 and HiSeq X instruments and moving all sequencing to the NovaSeq platform. This means there will be some changes in our pricing and order model and we will keep you updated. Meanwhile, if you have any questions of how this will affect your research don’t hesitate to get in contact with us at

We are looking forward to an exciting new year and wishing you all a happy holidays!

Christmas holiday 2018 (2018-12-08)

NGI Portal
Projects submitted before 11:00 AM on Tuesday December 11 will be processed in time for sample delivery before Christmas.

NGI Stockholm
The last day for sample delivery is Friday 21st of December. Sample deliveries can be resumed from Jan 7th.

NGI Uppsala - SNP&SEQ (Illumina)
The last day for sample delivery is Friday 21st of December, 9-11 AM.

NGI Uppsala - UGC (PacBio/IonTorrent/Sanger)
The last day for sample delivery is Tuesday 18th of December.

The New NovaSeq 6000: Costs, indexing and strategies (2018-09-17)

Date: September 25th, 9-11 in Gamma 2 lunchroom, SciLifeLab Solna. Talks from IDT, Illumina, and SciLifeLab staff. Coffee and breakfast provided. Topics include: Pricing updates at NGI, project pooling policies, choosing indexes for large flow cells, and avoiding index hopping. You will also have the chance to talk to representatives from IDT and Illumina, as well as meeting our project coordinators to plan your upcoming projects.

Free registration for breakfast

BiG Talks – Bioinformatics and Genomics Seminar Series (2018-05-31)

Date: June 11, 10.30-11.30 in Trippelrummet, Navet, SciLifeLab Uppsala and online Title: Genome sequencing of 15,000 healthy elderly Australians: implications for clinical genetics Speaker: Dr. Paul Lacaze, Head of the Public Health Genomics Program, Monash University, Melbourne Australia

The ASPREE Healthy Ageing Biobank contains ~15,000 consented samples from individuals aged 70 years or older participating in the ASPirin in Reducing Events in the Elderly (ASPREE) study – Australia’s largest clinical trial and longitudinal study of healthy ageing. All ASPREE biobank samples are being sequenced using a targeted ‘super-panel’ of 750 genes used commonly in clinical testing, Over 11,500 samples have been sequenced (May 2018), identifying hundreds of actionable pathogenic variants in individuals lacking any apparent signs and symptoms of genetic disease beyond 70 years. Results will be presented on these findings, with implications for our understanding of penetrance and clinical actionability for genes used in routine testing. BiG Talks – Bioinformatics and Genomics seminar series arranged in collaboration with SciLifeLab platforms NBIS, NGI and CG

For more information and to register, please visit the SciLifeLab website.

Summer 2018 (2018-05-16)

Order processing and sample submission for sequencing will be closed during summer. Library preparation and sequencing will continue at a reduced pace.

  • Order submission at the NGI Order portal will be closed from June 18 to August 6. Only complete orders will be processed at June 18.
  • Sample submission will be closed from June 29 to August 6.
Director and Co-Director positions for SciLifeLab genomics and high-throughput sequencing (2018-04-16)

Are you a visionary researcher within genomics with experience of operating or supervising infrastructures? Are you ready to take a major leadership roles in genomics? SciLifeLab now seeks a Director and a Co-Director to head the national Genomics Platform and high-throughput sequencing. An expressions of interest to these positions from both national and international candidates are welcomed!

Read more at SciLifeLab website.

Vacancies: Forskningsingenjör (vikariat) at NGI Uppsala (2018-04-16)

Är du en utbildad biotekniker, molekylärbiolog eller liknande med hög noggrannhet, ansvarskänsla och god samarbetsförmåga? Har du praktisk erfarenhet av storskaligt laboratoriearbete, gärna i ackrediterad miljö och med datorstyrda laboratorieinstrument? NGI Uppsala söker nu en forskningsingenjör till sekvenseringsenheten av SNP&SEQ-teknologiplattformen. Arbetet omfattar DNA-sekvensering med modern instrumentering från Illumina såsom HiSeqX, NovaSeq, HiSeq2500 och MiSeq.

Läs mer om tjänsten och ansök på UU hemsida.

Vacancies: 2 Bioinformaticians at NGI Uppsala (2018-04-11)

Do you want to work in one of the world’s fastest growing technology areas? NGI Uppsala (the SNP&SEQ Technology Platform)are currently looking for two bioinformaticians responsible for managing and analyzing the sequence data produced by the platform, as well as the development and maintenance of pipelines for data analysis.

Read more and apply at UU website.

Vacancies: Project coordinators at NGI Stockholm (2018-04-11)

Would you like to work in a dynamic environment in one of Europe's largest sequencing centres? Are you service minded molecular biologist with good communication and organizational skills who would like to work in an area of rapid technology and application development? NGI Stockholm is right now looking for a Junior Project Administrator and a Project Coordinator.

Read more and apply at the KTH website

2018 10x Genomics User Group Meeting in Uppsala (2018-02-21)

Are you interested in learning more about the Chromium System and Linked-Read Sequencing? 10X Genomics is organizing a User Group meeting at BMC, Uppsala on April 11-12, 2018. This will be a highly informative, action-packed event including both 10x and customer speakers, software demos, poster sessions, and evening dinner/entertainment. At the user meeting you will also get the chance to meet and listen to representatives from NGI.
For more information and to register, please visit the event website: 2018 User Group Meeting

Improving accessibility to data deliveries (2018-02-12)

Now we have improved the accessibility to the delivered data! By default, the bioinformatic contact person appointed by the PI on the sequencing or genotyping order will now have access to the delivered data, in addition to the PI. Previously, the PI was the only person with access to the data and he or she had to explicitly grant access to additional persons. This requires that the persons with access to the data have registered an account in SUPR and the email addresses on the order are the same as the ones used when registering the account.

33 milion SEK to support and advance large-scale genomic research in Sweden (2017-12-05)

The SciLifeLab Board has announced its decision on funding 14 projects within the SciLifeLab National Sequencing Projects initiative. The aim of the initiative is to support and advance large-scale genomic research in Sweden within both health and biodiversity by providing sequencing support to scientists through open calls. Thereby supporting them in carrying out competitive international research.

The grants are awarded as a deduction of costs for sample processing and sequencing at the National Genomics Infrastructure (NGI) and the Microbial Single Cell Genomics facility. The total sum awarded is 33 million SEK and will result in the sequencing of thousands of genomes within the projects by NGI.

New sequencing system (2017-07-12)

The NovaSeq6000 sequencing system (Illumina Inc.) is now installed at the NGI facilities in Uppsala and Stockholm.

The NovaSeq, launched by Illumina early 2017, offers high-throughput sequencing across the full range of DNA- and RNA-sequencing applications including transcriptome profiling, target re-sequencing, low coverage genome sequencing and single cell applications. By acquiring the NovaSeq6000 NGI will continue to offer the most cost efficient sequencing service to our users. Whole genome sequencing at a coverage of at least 15x will continue to be run on HiSeqX as the most cost efficient approach. During the summer and beginning of the fall, the NovaSeq systems will be validated and NGI aims to accept projects from users from September 2017. Projects already submitted and scheduled for HiSeq2500 may be transferred to the NovaSeq, in those cases the NGI project coordinators will contact the user for a discussion. You can read more about the NovaSeq system at the Illumina website.

New data delivery system (2017-06-21)

In mid-June, NGI will start introducing a new, secure system for delivering sequence and genotype data to users. With this new system, once your project is ready, you will be given access to a secure delivery server where your data will be available for download for a limited period of time.

For more information, please visit the Data delivery webpage

SciLifeLab offers funding for national genomics studies (2017-04-26)

SciLifeLab welcomes applications for Swedish research projects based on next generation DNA sequencing. In total, this third call will provide 30 million SEK in support for sequence analysis of unique and well-characterized sample collections to study either the genetic basis of disease or environmental effects on biodiversity.

Please go to this link for further instructions on how to apply.

Illumina NeoPrep system is being discontinued (2017-03-28)

Earlier this year Illumina informed us that the NeoPrep library preparation system will be discontinued (PDF). This method has been in use at the NGI Stockholm facility during the last couple of years and is now being replaced by other methods.

The Lucigen prep is still in the process of being validated but we feel confident it will be a good replacement for both the NeoPrep system and eventually also the regular PCR-free prep (Illumina TruSeq).

Illumina lowers the minimum average coverage requirements for HiSeqX to 15X (2017-01-12)

Illumina has recently updated the Special Conditions of Sale applicable to their HiSeqX instruments. The new Special Conditions lowers the requirements for average depth of coverage and now permits whole genome sequencing (WGS) and bisulphite sequencing down to an average depth of 15X coverage or greater.

The HiSeqX instruments are for many projects at NGI the most affordable Illumina instruments for WGS and bisulphite sequencing since it produces on average over 120 Gb of data per lane. However, many projects have been restricted by the previous conditions that WGS and bisulphite sequencing, of a sample isolated from a single species, had to reach an average depth of coverage of 30X or greater. The new requirements of 15X coverage or greater is therefore a substantial reduction which will make HiSeqX to an even more affordable and attractive alternative for many of our users.

The change applies from January 10 and onwards. Please contact one of our NGI project coordinators for further information and prices.

Christmas Holiday Period 2016 (2016-11-22)

Orders submitted after December 14 will not be processed until after the holiday break. Sample submission will be closed during the following period:

  • NGI Stockholm, Thursday 22 December - Friday 6 January
  • NGI Uppsala, Monday 17 December – Friday 6 January
The first map of genetic variation in Sweden (2016-10-20)

The first map of genetic variation in Sweden has now been presented. The results are based on whole genome DNA sequencing of 1 000 individuals, selected to cover the variation in the whole country. Thanks to this Sweden now has a national resource, which will facilitate research and diagnostics of genetic diseases. Project leader is Ulf Gyllensten, director of NGI Uppsala (Uppsala Genome Center), Uppsala University and the whole genome sequencing was performed at NGI Stockholm and NGI Uppsala (SNP&SEQ Technology Platform). You can read more about this new national resource at the SciLifeLab website

Current status for Stockholm node of NGI Sweden (2016-09-12)

The current status of operations can now be viewed in a graphical display. See the link in the text on the upper right of this page.

Project information updates (2016-07-06)

Several items of information are now updated in the orders. This includes project id, project name, and status which are fetched daily from the internal systems at the Stockholm node.

Phil Ewels' MultiQC tool published (2016-06-17)

"We present MultiQC, a tool to create a single report visualising output from multiple tools across many samples, enabling global trends and biases to be quickly identified. MultiQC can plot data from many common bioinformatics tools and is built to allow easy extension and customization." The paper (Open Access) is here and the documentation for the software (Open Source) is here.

Invoice address filled in automatically (2016-05-23)

If you set the invoice address and reference for your account, it will now automatically be filled in for any order you create. This does not apply to orders you clone; the information from the old order is used in that case.

Current best practice for de novo genome analysis (2016-05-20)

NGI Sweden and NBIS have created a document describing current best practice for de novo genome analysis. See the Documents page.

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