HiSeq X FAQs

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 HiSeq X Series Specifications.

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.

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.

Use either the TruSeq Nano DNA or the TruSeq DNA PCR-Free library prep kits. An insert size of 350 bp or 450 bp is supported. For more information, see HiSeq X System Compatible Products.

Illumina does not support other library prep methods or alterations to Illumina protocols, nor guarantee system performance with nonsupported methods.

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.

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

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.

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

A patterned flow cell has billions of ordered nanowells 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 eight lanes and has the same general dimensions as a HiSeq high-output flow cell.

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.

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 ×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.

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.

Supported read lengths for the HiSeq X are up to 2 x 150 bp plus two index reads of 8 bp each.

HiSeq X Control Software v3.5.0 (or later) supports 8 bp single indexing and 8 bp dual indexing. Dual-indexed sequencing on the HiSeq X System requires HP14, an i7 and i5 primer mix. For more information, see the HiSeq X System Guide.

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

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

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 Sequence Hub.

Use HiSeq X Control Software v3.1 or later with the HiSeq X Reagent Kit v2 or HiSeq X Reagent Kit v2.5. Sequencing TruSeq DNA PCR-Free libraries requires v3.1.

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