SGT Ordering

How ordering works

To see prices and place an order for our Next-Generation Sequencing services (including library prep), please use our Laboratory Information Management System (LIMS), DUGSIM: Duke University Genome Sequencing Information Manager. At any stage in DUGSIM, you can hover over the help icon for more details. For questions about this process, please contact us.

Start DUGSIM  

If you have any project design or technical questions, you can contact us by email or schedule a consultation:

Consultation Request

Step 1:

Create an Account in SeqLIMS

SeqLIMS header screenshot; Duke University School of Medicine

  1. Go to SeqLIMS and click on "Sign up."

  2. Enter name, email for username, and password.


Screenshot from SeqLIMS; Sign up for an account. Shows a form to fill out available on the SeqLIMS page

*Checkmark Duke Affiliate? Enter your Duke NetID, if you have one. Otherwise, leave the textbox empty.


Get an Official Quote (Account Required) 

  1. Log into SeqLims
    SeqLIMS header screenshot; Duke University School of Medicine
  2. Click on "New Project"

    SeqLIMS navigational menu. From left to right: start, new project, quotes, orders, invoices, q&A, contact staff
     
  3. Click the drop-down menu for "Service" and choose sequencing platform
    Screenshot in SeqLIMS to estimate cost of a new project
     
  4. Select the type of sample for submissionScreenshot in SeqLIMS showing a drop down menu

     

  5. For each sample type, input the sample quantity, sequencing product, and sequencing product quantity. while submitting specimens, also select specimen-processing product, if nucleic acid extractions from sample are required, and library-preparation product for the type of library build.
    Screenshot in SeqLIMS of the number of specimens you plan to submit and products you need.
     
  6. Click on the "Estimate quote" button at the bottom of the page.

    SeqLIMS screenshot of button that says estimate cost
  7. Review the estimate cost. Enter a project name, additional notes, questions, or information, if any, and click on the "Request quote" button at the bottom of the page.SeqLIMS screenshot with project name, note, and button to request quote
  8. Our staff will review and process your request within 24 hours.

Place an Order (Quote Required) 

  1. You will receive an email from SeqLIMSof your approved quote.

  2. Sign into SeqLIMS.
  3. Go to the "Main" page and locate your quote.

    SeqLIMS screenshot of your quotes
  4. Scroll to the bottom of the page and directly place an order from the approved quote by clicking "Convert quote into order."
    SeqLIMS screenshot: Actions: Save quote, convert quote into order, copy quote, printable version of quote*Non-Duke customers must also include information of an authorized representative of your institution, that is, a person able to bind the institution to the agreement.
    SeqLIMS screenshot of the authorized representative form
  5. Once an order is placed and we have validated the mode of payment (reception of your Purchase Order or valid Fund Code), a project will be assigned a unique order number. We do not accept credit cards.

Step 2: 

Prepare Your Sample(s) (Order Required)

*We will return samples that are not properly prepared and/or submitted

  1. Sign into SeqLIMS.

  2. Go to the "Main" page and locate your order.
  3. Click on the "Edit samples etc." button to fill in information about your samples. 
  4. Prepare your samples according to the Sample Requirement page – we will return samples that are not properly prepared and/or submitted

 

Submit Your Sample(s) (Prepared Samples Required)

  1. Print a copy of your unique order number (not quote) and place that with your samples
  2. We have three ways to submit your samples
    1. Duke’s Campus:
      • *email microbiomesr@duke.edu to coordinate drop off
        MSRB3 - 3 Genome Ct., Durham
        Mondays - Tuesdays, 2 - 3 p.m
        **Any biological samples that need extraction services must be dropped off at Chesterfield and NOT MSRB3
         
    2. Direct Drop Off
      Chesterfield Bldg - 701 W. Main St, Suite 320
      Mondays - Thursdays, 10 a.m - 4 p.m.
      Fridays 10 a.m. - 12 p.m.
       
    3. Ship
      Attn: Sequencing Order [#xxxx]  
      GCB Sequencing and Genomic Technologies Shared Resource
      Chesterfield Bldg.
      Duke University
      701 W. Main Street
      Suite 320,
      Durham, NC 27701
      USA

Data Delivery & Processing

Step 3:

  1. We deliver your data in the form of demultiplexed FASTSQ files via an sftp server. We will send you login and password information to access the data via email. To share data with collaborators, you can simply forward the email containing the login and password information. Data is retained for thirty days. Please reach out to us about delivering demultiplexed 10x data.
    • Most sequencing runs performed today are paired-end. This means you have a file from both ends of the insert - read 1 (R1) and read (R2). If your order was on more than one lane, each lane will produce a separate sequencing file also (L001-L004)
  2. Beyond delivery of FASTQ data, we provide basic data processing for $97/hour. Contact us for more information:
    • Mapping and Basic QC
    • RNA-seq data processing
    • Variant calling
    • Peak calling
  3. For all publications that include data generated in the Sequencing and Genomic Technologies Core Facility, we kindly request that you acknowledge this support:

    We thank the Duke University School of Medicine for the use of the Sequencing and Genomic Technologies Core Facility, which provided ______________ service.