Placing an order
An order is a request for sequencing/genotyping of a set of samples that are to be handled in a homogenous fashion. If you have a set of samples that you wish to analyze using more than one type of sequencing/genotyping application, then you must submit one order for each sequencing/genotyping application.
See How to place an order for more information on how to submit your order.
If you have not used the services of the NGI before, or if you wish to use a new sequencing/genotyping application, then you should request a planning meeting with NGI.
In this meeting, the experimental approach is discussed, to ensure that your expectations match what NGI SciLifeLab can offer, and that the experimental design is optimal. The meeting is free of charge.
See How to place an order for more information on how to proceed.
The best way to obtain information about the price for a project is to communicate with the relevant NGI node (see contact information).
For academic researchers, the price of a project is based on a consumables-cost principle: NGI will calculate the expected amount of reagents, consumables, etc, required for the order. Using the price of the reagents that NGI has to pay its vendors, a total cost for the project will calculated.
For commercial researchers, a fee covering all costs for NGI will be calculated.
All prices already include discounts for large numbers of samples.
NGI purchases reagents from its suppliers as cheaply as possible. This means that the discounts that can be gained from processing large number of samples are already obtained to the fullest possible degree. We have chosen to benefit all users equally, so the prices we charge researchers for reagent costs already include the discounts for the large numbers of samples sent in by all researchers as a collective.
The information provided by you when you submit an order is processed by the NGI project coordinators.
NGI will check the details of your information, and may contact you if there are any questions. When all issues have been resolved, NGI will prepare an agreement which will be sent to you.
You must sign and return the agreement to us. Samples must not be delivered to NGI unless a signed agreement has been sent.
An order always has a certain status, which describes at what stage it is in the workflow. The currently defined statuses are:
Note: The status of the samples for an order (project) is currently not available in this system. This feature is under development. Stay tuned.
You can read more about sample requirements and how to submit your sample at Samples delivery
Please go through the following checklist before submitting samples to the relevant NGI node.
When NGI has received: 1) a signed agreement, 2) the samples, and 3) valid sample information, the samples will be assigned an arrival date. Please note that NGi will not accept any samples without a project ID and a signed agreement.
An arrival Quality Control (QC) of samples will be performed within 10 working days of the arrival date. If the samples do not pass our QC we will let the researcher decide if replacement samples should be sent, or if NGI should proceed with the available samples. This decision has certain implications on how NGI handles the samples, see the agreement.
The samples are queued for subsequent steps when all samples have passed arrival QC. This date is the queue date.
NGI provides a set of pre-defined "Best practice" analysis packages for sequence data produced at SciLifeLab. These are specific for each sequencing applications, see this page for more information.
NGI Sweden does not provide any other analysis or help with bioinformatics apart from the Best practice analysis.
For more information, please visit our Bioinformatic support page.
NGI Sweden and NBIS have written a description of current best practice for de novo analysis. See the Documents page.
Providing bioinformatic support beyond our Best practice analysis is not included in the NGI mission.
For more information, please visit our Bioinformatic support page.
Our previous routine for data delivery required that you applied for a compute project on the HPC resource “MILOU” before placing an order at the NGI Order Portal, regardless if you needed any compute resources. Once data was ready for delivery, you were required to ensure that sufficient storage quota was assigned to the project. NGI would then deliver the data to an INBOX folder where you could access it. In addition to being an administratively heavy process for everyone involved (i.e. the user, NGI, UPPMAX/UPPNEX), this option was only available to Swedish academic users.
With the new delivery system, NGI will create the delivery project for you and deliver data to a dedicated storage resource, from which you can retrieve it. You need to have registered in SUPR but other than that, you don’t need to apply for any resources in order to receive data. This option is also available to all users, not only Swedish academia. You can read more about our data delivery system on the data delivery webpage
No. UPPMAX provides a mechanism to transfer data from GRUS to your Bianca or Rackham project with minimum effort. See the Deliver user guide for details.
After 90 days, the delivery project will expire and will be automatically removed from GRUS.
The responsible NGI facility, see the Contact page
For Swedish academia, SNIC provides resources that you can apply for.
This means that NGI has started delivering data to you and you will receive further information from NGI shortly. You can also log in to the SUPR web interface and view the project details, add project members etc.
You should download the data from GRUS (see instructions). Any member of the delivery project can access and download the data. Initially, the PI and the bioinformatics responsible person are the only members of the delivery project. The PI can add more members to the delivery project using the SUPR web interface. If you have questions regarding retrieving data from GRUS, please contact firstname.lastname@example.org.
Use the supplied md5 checksum files to verify the integrity of the data after download. A typical command for this would be
md5sum -c file_with_checksums.md5 but the exact command may vary depending on the tool used and the format of the md5 checksum file. You should ensure that the verification doesn't report any inconsistencies and that all files have been verified.
In any and all publications based on data from NGI Sweden, the authors must acknowledge SciLifeLab, NGI and Uppmax, like so:
The authors would like to acknowledge support from Science for Life Laboratory, the National Genomics Infrastructure, NGI, and Uppmax for providing assistance in massive parallel sequencing and computational infrastructure.