Genome Sequencing Facility in the News

The enhanced sequencing performance of HiSeq 3000 is enabled by two new technologies: patterned flow cell and kinetic exclusion amplification. These two new technologies were only available on the X Ten sequencers for a single application, the re-sequencing of human genomic samples. In contrast to the random clustering employed previously (HiSeq 2500 and earlier models), the clusters in HiSeq 3000 are now generated in ordered nano-wells to allow for higher cluster densities and unambiguous cluster identification. Unlike Illumina X Ten line dedicated to human genome re-sequencing only, HiSeq 3000/4000 series are capable of processing samples derived from all organisms, making them very flexible and cost-effective sequencing platforms. The decreased cost and the increased capability will significantly benefit every user’s sequencing need and bring the type of genomic analyses once possible only in large-scale sequencing centers to research laboratories both large and small, and make scientific and translational genome sequencing applications closer to reality.


The table below compares with HiSeq 3000 (current) and HiSeq 2000 (previous)

For 50bp single reads sequencing
(most RNA-seq and ChIP-seq)

Instrument Run time1 # of reads/lane
(millions)
Read Length
(base-pair)
>Q30 Note
HiSeq 3000
(current)
12 hour 300-400 50 90-95% New Chemistry
HiSeq 2000
(previous)
3 days 150-190 50 90-95% V3 Chemistry3

For 100bp paired end sequencing
(most exome-seq and RNA-seq for splicing variants)

Instrument Run time1 # of reads/lane
(millions)
Read Length
(base-pair)
>Q30 Note
HiSeq 3000
(current)
<2 days 600-800 100 90%-95% New Chemistry
HiSeq 2000
(previous)
11 days 300-380 100 85%-90% V3 Chemistry3

The GSF has purchased HiSeq 3000 in May and installation and training have been completed in June 2016. If you are considering next generation sequencing for your research, please contact Dr. Zhao Lai for consultation on experimental design, pricing and scheduling.