Illumina Next Seq 500

Illumina offers innovative next-generation sequencing (NGS) platforms that deliver industry-leading data quality and accuracy, at an unparalleled scale. The NextSeq500 is the right sequencer for any project size. It is the only desktop sequencing system capable of sequencing a high coverage (30x) whole human genome in one run. The flexible throughput means no waiting to fill a flow cell and thus a quicker turnaround time for your sequencing sample.

Because of high and mid output options the Next Seq can easily shift between high and low throughput projects. There are five options with the NextSeq500:

 NextSeq500 Flowcell Options Avg Output (Gb) / Run  Reads (M)/ Run  Avg Read Length (bp)
 NextSeq 500 Mid Output v2 (2x75) 16-19G 132 150
 NextSeq 500 Mid Output v2 (2x150) 32-39Gb 132 300
 NextSeq 500 High Output v2 (1x75) 25-30Gb 400 75
 NextSeq 500 High Output v2 (2x75) 50-60Gb 400 150
 NextSeq 500 High Output v2 (2x150) 100-120Gb 400 300


We offer library preparation services, barcoding services, and sequencing services. We highly recommend that the first step in considering running Illumina sequencing is to meet with a bioinformatics specialist to work out your experimental design, decide which library prep would suit your experiment best, and select the NextSeq500 sequencing option that would give you the coverage you need. The importance of meeting with a bioinformaticist prior to your sequencing run cannot be over-stated.

Illumina NextSeq 500 Sample Submission Guidelines

  • Please read the guide for entering a job request on our dnaTools server How to use dnaTools for NextGen Sequencing
  • NOTE: As of December 1, 2016 all UNR & NSHE labs need to purchase the requested flow cell kit(s) from Illumina and submit the kit(s) along with their samples. If you have questions about purchasing your flow cell kit(s), please contact NGC.
  • Before submitting a job request, your lab PI must generate an account with Illumina BaseSpace (  ). On completion of the sequencing run, the data ownership will be transferred to the PI’s account.
  • If submitting a library prepared in your lab, please refer to: Illumina Prepared Library Sample Submission Guidelines  
  • Illumina has many library kit options. We highly recommend you work with a bioinformaticist in the design of your experiment and selection of a library prep kit. A helpful website is Illumina’s Library Prep and Array Kit Selector: . This tool will help you determine the best kit for your needs based on your project type, starting material, and the method or application.
  • Illumina has a number of options for adding indices to your library. Some helpful information can be found in:
  • What we do does not improve the quality of your sample. The integrity of your sample is crucial to the success of any downstream processing. While we make every effort to generate successful sequencing runs with high quality data output, we cannot be responsible for improperly prepared samples. Therefore, we can make no guarantees as to the quality and quantity of output if:
    • Libraries were prepared by the user (we have minimal control over the library quality).
    • Samples submitted for library preparation do not meet minimal requirements.
    • The user has opted to not amplify the library as part of the library preparation.

Illumina NextSeq Data

  • The data files generated in NextSeq500 sequencing are not accessible through the dnaTools server; rather they are uploaded to your Illumina BaseSpace account. Your Illumina BaseSpace account information will be required at the time of sample submission. The data from an Illumina sequencing run is too large for NGC to store; your lab is responsible for downloading and backing up the data. Once the data is received into the PI’s BaseSpace account, the lab PI may then transfer or share the data with others in the labs or with collaborators.
  • The next generation sequencing data generated will require further analysis and it is the responsibility of your lab to arrange for bioinformatics services. We highly recommend that the first step in considering running next gen sequencing is to meet with a bioinformatics specialist.
  • Illumina’s BaseSpace has over 50 apps for data analysis. There is a fee for use of these apps, but these are a good first step in data analysis. No one knows better what you are looking for in your data and we encourage each scientist to run as much of the data analysis themselves as possible.
  • NGC does not provide bioinformatics services.
    PDF instructions for the CLC-Bio Genomics Workbench can be found here: .
    Once you have viewed the instructions if there is something you are interested in running please email to set-up a time when you can stop-by the lab and we can assist you in setting-up the analysis.