HiSeq 4000 FAQs

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  • Libraries


  • Like the HiSeq 2500 System, the HiSeq 4000 is designed as an open platform intended to support a broad array of applications. Internally, Illumina has run numerous library prep kits without issue. For sample data demonstrating system performance, see the HiSeq 3000/4000 Sample Datasheets.

    The HiSeq 4000 system is compatible with current paired-end P5 and P7 primers. Single-read and paired-end libraries are compatible with the HiSeq 4000, but must use current adapters. Legacy libraries that are based on the original Illumina single-read adapter do not cluster properly.

    True low-diversity samples, such as single amplicon and 16S samples, are not expected to produce quality results. However, spiking in a well-balanced genome such as PhiX improves performance.

  • Reagents and Flow Cells


  • 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 3000/4000 patterned flow cell has eight lanes and the same general dimensions as a HiSeq high-output flow cell.

    Reagents and flow cells provided in the HiSeq 3000/4000 SBS Kit and the HiSeq 3000/4000 Cluster Kits are designed and optimized for the HiSeq 4000 and HiSeq 3000 systems. Reagent kits designed for other HiSeq systems are not compatible with the HiSeq 4000 and HiSeq 3000 systems.