News

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

Summer Holiday Period 2017 (2017-05-22)

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

  • Orders submitted will be closed from June 22 to August 7
  • Sample submission will be closed from July 3 to August 7. (Last day for sample submission is June 30).
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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