New data delivery system
2017-06-22
In mid-June all facilites within NGI, including the SNP&SEQ Technology Platform, 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.
Delivery projects
In order to administer access to the delivery server (named “GRUS”), we have introduced a new type of project called “delivery project”. A delivery project exists only on GRUS and for the purpose of delivering data from NGI to users. It is therefore read-only and has no associated core hours or quota limitations to take into consideration. For extra security, two-factor authentication is required to access the data in the delivery project.
Data delivery
Once a sequencing or genotyping project is ready, NGI will register a delivery project in SUPR for the delivery. The PI of the sequencing or genotyping project will also be the PI of the corresponding delivery project. This means that you are no longer required to have a pre-existing SNIC/UPPNEX project account prior to submitting an order - NGI will create the delivery project for you. If you wish to use SNIC resources for downstream data analysis, you just apply for a SNIC/UPPNEX project the usual way.
Data retrieval
The delivery project is administered in SUPR just like any other SNIC or UPPNEX project. In other words, the PI can use the SUPR web interface to e.g. add or remove users and thereby grant access to the project data. Once you have been granted access to a delivery project, you can download data to your preferred location* using e.g. sftp transfer. If you wish to download data to a SNIC/UPPNEX resource, there will soon be an option to have this done automatically in SUPR. Please see the GRUS user guide for further details.
You can also read about the new data delivery system at the NGI Order portal.
* If your preferred location is located outside the SUNET network, you need to submit a ticket to support@uppmax.uu.se and request that your IP-address should be whitelisted.
News and events
-
SNP&SEQ sample submission summer 2023
The last day for delivering samples to our sample reception before the summer break is Thursday 22nd June.
-
PacBio Revio Launch Event
Join us for our PacBio Revio release event, with invited speakers from PacBio and the research community
-
Honoring Professor Ann-Christine Syvänen, former director of the SNP&SEQ Technology Platform
Celebrating the progress in Human Genomics during the past three decades: From PCR to Precision Medicine
-
The sample Drop-off is closed on Friday April 7th and Friday May 19th 2023
-
Limited Capacity over the Winter Holidays 2022-2023
-
Summer 2022 - Opening hours and sample deliveries
Information about sample drop-off and other activities during the summer at NGI Uppsala - SNP&SEQ (Illumina samples)
-
March 30th: NGI and Nanopore tech update seminar
NGI and Oxord Nanopore are giving a joint seminar with invited speakers to update our users on the latest technology developments.
-
Results from the Sequencing Quality Control 2 (SEQC2) initiative published
NGI contributes to SEQC2 initiative through ongoing participation in EATRIS-ERIC.
-
Summer 2021 - Opening hours and sample deliveries
NGI will be operating at a limited capacity during summer, and a number of our user-targeted activities will encounter delays between week 25 and week 32 (June 24, 2021 – Aug 9, 2021). All services will resume as usual on August 9, 2021.
-
NGI is the first European certified service provider for the Olink Explore platform
NGI in collaboration with the SciLifeLab Affinity Proteomics Uppsala unit now offer protein biomarker analysis services using the Olink Explore assay.
-
Sample Drop-Off is closed on Friday April 23, 2021
-
Limited opening hours for sample delivery in person as of January 2021
Due to the current pandemic, the reception for Sample Drop-off will be limited to Fridays only (open hours 09-11:00), until further notice.
-
Important information regarding sample drop-off during ongoing pandemic
-
PromethION launch event
With the introduction of nanopore sequencing as a service at NGI Uppsala, we invite all our users to a virtual PromethION launch party at June 11th. Register now to join, and to participate in the PromethION prize draw.
-
New NGI website
The National Genomics Infrastructure NGI is pleased to announce the launch of our new website with more thorough information on our services.
-
Jessica Nordlund receives “Stora Gustafssonpriset”
Congratulations to our facility director Jessica Nordlund for recieving the “Stora Gustafssonpriset” in medicine 2020 for her research on acute lymphoblastic leukemia!
-
New services at UGC
Uppsala Genome Center now offers sequencing with Nanopore and Sequel II. We have also launched our DNA extraction service.
-
Opening hours for Sample Drop-off during public holidays - spring 2020
Information about samples submission at NGI Uppsala - SNP&SEQ (Illumina samples) during public holidays - spring 2020
-
Christmas holiday break
Project and sample submission deadlines to Uppsala Genome Center before christmas.
-
Sample submission during Christmas season 2019
Information about order and samples submission at NGI Uppsala - SNP&SEQ (Illumina samples) before Christmas 2019.
-
EATRIS-Plus
SNP&SEQ facilty is now a EATRIS-Plus partner.
-
Renewed accreditation
The SNP&SEQ technology platform is accredited according to ISO/IEC 17025:2017.
-
Sample submission at NGI Uppsala (SNP&SEQ) May + June 2019
Sample drop-off for Illumina sequencing at NGI Uppsala (SNP&SEQ) before summer 2019.
-
Long-Read Sequencing Meeting 2019
It is our pleasure to invite you to our Fourth Long-Read Sequencing meeting that will take place at BMC Uppsala on April 3-4 this year. Registration is now open!
-
PacBio Sequel update
PacBio's high thoughput system Sequel has now replaced the older system RSII.
-
Capillary Electrophoresis Services at UGC soon to be discontinued
From January 18th, 2019, Uppsala Genome Center will no longer offer Sanger sequencing, fragment analysis, or genotyping with STR markers. The last day to submit plates for capillary electrophoresis is January, 15th.
-
Christmas holidays break
Uppsala Genome Center is closed during the Christmas holidays. You can find our closing and opening times here.
-
Our new iSEQ has arrived
The SNP&SEQ Technology Platform is happy to inform that we now have a new instrument at our platform. The iSEQ is currently being installed at the platform.
-
Sample Drop-off closed on Midsummer's Eve
The Sample Drop-off for sequencing at the facility will be closed on Midsummer's Eve, Friday, June 22.
-
Summer 2018 Opening hours
Order processing and sample submission will be closed during summer. Library preparation and sequencing will continue at a reduced pace. See below for important deadlines for sample submission and ordering.
-
Extra IMV Seminar with Dr. Caroline Heckman, FIMM
NGI Uppsala - the SNP&SEQ Technology Platform would like to welcome you to an interesting extra IMV Seminar about precision treatment strategies and drug resistance.
-
Forskningsingenjör, NGI Uppsala SNP&SEQ-teknologiplattformen
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? Vi söker nu en forskningsingenjör till sekvenseringsdelen av SNP&SEQ-teknologiplattformen.
-
Two bioinformatics positions at the SNP&SEQ Technology Platform
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.
-
Easter 2018 Opening Hours
The Sample Drop-off for submitting samples to the facility sequencing service is closed for the Easter Holidays at the following dates:
-
Drop-in consultation with NGI.
Are you planning to apply for sequencing support from VR or Formas this year? Struggling with the experimental design, costs and time lines of your sequencing project to be able to write an attractive and accurate proposal and budget? Welcome to NGI drop-in consultation!
-
10X Genomics is arranging a User Group Meeting in Uppsala
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.
-
Celsius-Linneaus Lectures and Symposium in Uppsala
NGI welcomes all researchers with an interest in transcriptomic and single cell studies to this year's Celsius-Linneaus Lectures and Symposium.
-
Christmas Holiday Period 2017
Order processing and sample submission for sequencing will be closed during Christmas holiday. Library preparation and sequencing will continue at reduced pace.
-
33 milion SEK to support and advance large-scale genomic research in Sweden
SciLifeLab has announced giving 33 million SEK to 14 sequencing projects focused on human whole genome sequencing and biodiversity under the SciLifeLab National Sequencing Projects initiative. In total, thousands of genomes will be sequenced within the projects by the National Genomic Infrastructure, NGI.
-
Developers of the Arteria Project at SNP&SEQ interviewed by StackStorm
Developers of the Arteria Project at SNP&SEQ Technology Platform was recently interview by StackStorm for being innovative StackStorm Community Thought Leaders. StackStorm is an open-source automation platform that connects apps, services and workflows and has been used as a base within the Arteria project.
-
Long-read sequencing meeting and workshop
NGI Uppsala invites you to join a two-day event dedicated to long-read sequencing applications.
-
Single cell RNA-seq seminar
The SNP&SEQ Technology Platform (NGI Uppsala), Miltenyi Biotec, and 10x Genomics welcomes all researchers with an interest in single cell sequencing.
-
New data delivery system
In mid-June all facilites within NGI, including the SNP&SEQ Technology Platform, 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.
-
The NovaSeq system arrives at the SNP&SEQ Technology platform
The SNP&SEQ Technology Platform has acquired the newly launched NovaSeq6000 sequencing system (Illumina Inc.) and the instrument is currently being installed.
-
Summer Holiday Period
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).
-
New sample submission routines for Illumina sequencing
From March 13, 2017 the SNP&SEQ Technology platform will change its routines for sample submission for Illumina sequencing.
-
Illumina lowers the minimum average coverage requirements for HiSeqX to 15X
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.
-
Novel library preparation for whole genome DNA methylation sequencing
-
The first publication based on the new Methylation EPIC array from Illumina has been released
The 850K array demonstrates high reproducibility at the 450K CpG sites, is consistent among technical replicates, is reliable in the matched study of fresh frozen versus formalin-fixed paraffin-embedded samples and is also useful for 5-hydroxymethylcytosine.