Frequently Asked Questions (FAQ)

What is 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.

What is a planning meeting?

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.

What does a project cost?

The best way to obtain information about the price for a project is to communicate with the relevant NGI node (see contact information).

What is NGI sequencing and genotyping prices based on?

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.

Can I get a discount if I have many samples?

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.

How is an agreement prepared?

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.

What does the order status "Preparation", "Submitted", etc, mean?

An order always has a certain status, which describes at what stage it is in the workflow. The currently defined statuses are:

  • Preparation
    The order is being prepared by the researcher. It has not yet been submitted to NGI. Please note that NGI will not even look at an order that is in preparation. The researcher must submit the order before NGI will consider it.
  • Submitted
    The order has been completed by the researcher and submitted for NGI to review. The researcher cannot edit an order when it has been set to this state. If you wish to modify it, you need to contact NGI.
  • Review
    The submitted order is being reviewed by a NGI facility to check for coherence and feasibility. NGI will also decide which node to allocate the project to. The researcher will soon receive a response.
  • Accepted
    The order has been accepted by NGI SciLifeLab. A research agreement is being prepared specifying the price and other details of the project. The agreement will be sent to the researcher for signature. The researcher must return the signed agreement to the relevant NGI facility.
  • Rejected
    The order has been rejected by NGI for some reason or another.
  • Processing
    A NGI facility is working on the order or processing your samples either in the lab or in data analysis.
  • Aborted
    The order or project has been aborted by the researcher, for whatever reason.
  • Closed
    All work and actions for the order have been performed.

Note: The status of the samples for an order (project) is currently not available in this system. This feature is under development. Stay tuned.

Submitting samples: what do I need to do?

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.

  • Fill in an order in this portal and submit it. NGI will prepare a research agreement and send it to you.
  • Sign the agreement and return to the NGI node.
  • Read the document “Sample requirements for genomics projects” for the relevant NGI node available in the Documents page.
  • Check the quality of your samples, and make sure that NGI's specifications are met.
  • Collect the required information about the samples as specified.
  • Deliver the samples and send the sample information to the relevant NGI node.

What happens after sample delivery?

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.

Can I get advanced bioinformatics support from NGI?

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.

What is current best practice for de novo genome analysis?

NGI Sweden and NBIS have written a description of current best practice for de novo analysis. See the Documents page.

Can I buy more bioinformatics analysis from NGI?

Providing bioinformatic support beyond our Best practice analysis is not included in the NGI mission.

For more information, please visit our Bioinformatic support page.

Previously, I had my data delivered to the INBOX of my UPPNEX project. How is the GRUS data delivery system different from that?

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

I will analyze my data on a SNIC-UPPNEX resource, do I need to use SFTP?

No. UPPMAX provides a mechanism to transfer data from GRUS to the UPPNEX project with minimum effort. See the GRUS user guide for details.

What will happen to my data on GRUS after 90 days?

After 90 days, the delivery project will expire and will be automatically removed from GRUS.

I have a question about the contents of the data delivery, who should I contact?

The responsible NGI facility, see the Contact page

I have a question on retrieving data from GRUS, who should I contact?

support@uppmax.uu.se

I have a question about working on Bianca/Milou/SNIC-UPPMAX, who should I contact?

support@uppmax.uu.se

I need to apply for compute resources, who should I contact?

For Swedish academia, SNIC provides resources that you can apply for.

How is my personal account data handled by NGI?

By applying for an account, you give your permission to NGI according to the Personal Data Act (Personuppgiftslagen 1998:204; PUL) to store and handle the personal account data entered by you. NGI will treat the data as confidential, and will not transfer it to any third party without explicit approval by you.

How do I acknowledge NGI in my publication?

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.