Questions & Answers

Expand All

General

  • What is the throughput of the HiSeq X system?

    Each system can generate 1.6–1.8 Tb in less than 3 days with greater than 75% of bases about Q30 from a 2 x 150 bp run. This throughput enables 16 genomes covered at 30x per run per system. For more information, see the HiSeq X system performance specifications page.

Libraries

  • What applications are supported on the HiSeq X system?

    The HiSeq X system is intended for large-scale whole-genome sequencing projects using either the TruSeq Nano DNA (HT or LT) or the TruSeq DNA PCR-Free (HT or LT) library prep kits. Other applications are not compatible or supported on the HiSeq X system.

  • What are the compatibility requirements for using supported library prep kits on the HiSeq X system?

    Sequencing libraries prepared with the TruSeq DNA PCR-Free Sample Prep Kit requires the HiSeq X Reagent Kit v2, or later. TruSeq DNA PCR-Free libraries are compatible only with workflow changes introduced with the v2 chemistry.

    Library Type

    Reagent Kit Version

    Control Software Version

    TruSeq Nano DNA

    Any HiSeq X kit version

    Requires v3.0, or later

    TruSeq DNA PCR-Free

    Requires the HiSeq X v2 kit, or later

    Requires v3.1, or later

  • What type of library prep methods are supported on the HiSeq X system?

    Use either the TruSeq Nano DNA (HT or LT) or the TruSeq DNA PCR-Free (HT or LT) library prep kits. An insert size of 350 bp or 450 bp is supported.

    For more information, see the HiSeq X Ten system kit page.

    Illumina does not provide support for any other library prep methods or alterations to Illumina protocols, or guarantee system performance with other than the supported library prep methods on the HiSeq X.

  • What is the recommended insert size for sequencing on the HiSeq X system?

    The supported insert size on the HiSeq X system is 350 bp and 450 bp for TruSeq Nano DNA and TruSeq DNA PCR-Free libraries.

Reagents and Flow Cells

  • What are the compatibility requirements for using the HiSeq X Reagent Kit v2.5?

    The HiSeq X Reagent Kit v2.5 requires HiSeq X Control Software v3.1, or later.

  • What flow cells and reagents are supported on the HiSeq X system?

    The HiSeq X system uses patterned flow cell technology. Reagents provided in the HiSeq X Reagent Kit are designed and optimized for the HiSeq X flow cell. Non-patterned flow cells and SBS kits designed for other HiSeq models have not been validated and are not supported for use on the HiSeq X system.

  • Can I use HiSeq X reagents on my other HiSeq system?

    No. HiSeq X reagents are designed and optimized for HiSeq X systems. HiSeq X reagents are not compatible with other HiSeq models.

  • What is a patterned flow cell?

    A patterned flow cell is a flow cell with billions of ordered nano-wells that are manufactured into the flow cell glass. The ordered wells allow for the generation of sequencing clusters in an ordered arrangement. Clusters are aligned more closely together increasing the number of output reads and amount of sequence data generated. The HiSeq X patterned flow cell contains 8 lanes and has the same general dimensions as a HiSeq high-output flow cell.

  • Can I use HiSeq X patterned flow cells on other platforms?

    No. HiSeq X flow cells are designed and optimized for use on the HiSeq X system. HiSeq X flow cells are not compatible with other HiSeq models.

  • How are the HiSeq X reagent kits configured?

    Each kit includes two flow cells and all required reagents, including clustering, SBS, paired-end, and indexing reagents. One kit provides consumables for a 150-cycle paired-end (2 x 150 bp) sequencing run plus indexing on both flow cell A and flow cell B.

    With the release of the HiSeq X Reagent Kit v2, a new kit configuration called the 10-pack kit is available. The 10-pack kit includes flow cells and consumables for 10 dual flow cell runs or 20 single flow cell runs. The 10-pack is designed to support the preparation and sequencing of 4 flow cells at a time, and significantly reduces storage requirements.

Workflow

  • Are there any workflow changes associated with the HiSeq X Reagent Kit v2.5?

    No. The HiSeq X Reagent Kit v2.5 has the same workflow introduced with the HiSeq X Reagent Kit v2. The HiSeq X Reagent Kit v2.5 uses the same library denaturation step during reagent preparation before clustering on the cBot. The denaturation step coupled with enhanced exclusion amplification (ExAmp) reagents enables sequencing of TruSeq DNA PCR-Free libraries on the HiSeq X system, in addition to superior data quality and coverage.

  • What sequencing read length is supported on the HiSeq X system?

    Supported read lengths for the HiSeq X are up to 2 x 150 bp plus single 8 bp indexing. Only single-indexed runs are possible on the HiSeq X system.

  • What indexing options are available on the HiSeq X system?

    Although the TruSeq Nano DNA and TruSeq DNA PCR-Free library prep kits are compatible with dual indexing, only 8 bp single indexing is supported on the HiSeq X system.

  • How long does a maintenance wash take?

    Actual wash time for a maintenance wash is approximately 1.5 hours, not including flow check time.

  • What is the delivered volume for a maintenance wash?

    Positions

    Delivered Volume

    8 SBS positions

    74 ml

    10 paired-end positions

    52 ml

    All positions

    15.75 ml per lane

  • How often do wash bottles and tubes need to be renewed?

    Monthly replacement of wash bottles and tubes containing maintenance wash solution is typically sufficient. Wash bottles and tubes containing water are typically replaced every 6 months, although the water is replaced about every week.

Software

  • Can I use Sequencing Analysis Viewer (SAV) to view data from a HiSeq X run?

    Yes. SAV 1.8.37, or later, is required to view data from a HiSeq X run. You can download SAV for use on a networked computer or use SAV in BaseSpace.

  • What control software version is compatible with current kits and library prep methods?

    Use HiSeq X Control Software v3.1, or later, with the HiSeq X Reagent Kit v2 or HiSeq X Reagent Kit v2.5. Version 3.1 is required to sequencing TruSeq DNA PCR-Free libraries.

    Library Type

    Reagent Kit Version

    Control Software Version

    TruSeq Nano DNA

    Any HiSeq X kit version

    Requires v3.0, or later

    TruSeq DNA PCR-Free

    Requires the HiSeq X v2 kit, or later

    Requires v3.1, or later

Analysis

  • What data quality can I expect from a run on the HiSeq X system?

    You can expect greater than 75% of bases above Q30 with a 2 x 150 bp run using the following libraries:

    • A human library prepared with the TruSeq Nano DNA Sample Prep Kit (350 bp or 450 bp insert)
    • A human library prepared with the TruSeq DNA PCR-Free Sample Prep Kit (350 bp or 450 bp insert)
    • Illumina PhiX control library