New HiSeq 3000 Sequencer In The Core

The Genome Center has acquired a HiSeq 3000 sequencer to be able to provide faster sequencing at significantly reduced per-base-costs. The new sequencer is already delivered and will be installed this week and then tested. Please note that for some samples the library preps should be adjusted for the HiSeq 3000.

The new sequencer is more than three times faster than the HiSeq 2500 and yields about 65% more reads per lane. For example the run-time of a paired-end 100 bp run is only 3 days on the HiSeq 3000 compared to 11 days on the HiSeq 2500. The number of reads per lane has improved from between 150-190 million (HiSeq 2500) to 260-310 million reads (HiSeq 3000). The maximum read length is 150 bp compared to 100 with the HiSeq 2500 High Output mode. Thus, the maximum yield per lane has more than doubled using the HiSeq 3000 and HiSeq 4000 sequencers (2.5x).

The progress is enabled by two new technologies: patterned flow cells and kinetic exclusion amplification (please see the video). In contrast to the random clustering employed previously, the clusters are now generated in ordered nano-wells to allow for higher cluster densities and unambiguous cluster identification. The HiSeq 3000 technology is derived from the human genome dedicated Illumina X10 line of sequencers.

In contrast to the X10, the HiSeq 3000 will sequence samples derived from all organisms. The flowcell is not appropriate for all types of libraries. For example the HiSeq 3000 system is not yet recommended for low-complexity sample sequencing (e.g. amplicons, GBS, or RAD-seq). A second limitation of the HiSeq 3000 is the restriction of library insert sizes to a max of about 500 bases (with average recommended insert size being 350bp or less). We can assist you in making your libraries HiSeq 3000 compatible.

The recharge rate per PE100 lane will stay the same as for the HiSeq 2500. The cost for a PE150 HiSeq 3000 lane will be the same as for a PE150 rapid lane. The cost for a SR50 lane will temporarily increase by $250 (HiSeq 3000 only; at UC rate) because Illumina does not offer yet single-end cluster kits and we will have to use the more expensive paired-end cluster kits. Illumina has promised to provide single end kits for the 3000 in the near future.

We will of course continue sequencing on our three MiSeqs as well as on the HiSeq 2500. The latter is of special interest for rapid runs (not available on the HS3000) which have increased in read length up to 250 bp paired end reads.


  • We have recently learned that the HiSeq3000/4000 sequencers have a very low tolerance for adapter-dimers. Shorter library fragments have an ever greater advantage during the kinetic exclusion amplification as compared to the bridge amplification chemistry.  There should be best none of them visible in your bioanalyzer traces.

The HiSeq sequencing queue is available online

Please find the HiSeq sequencing calendar as well as the sequencing queue now online at . On our website they are located under the Calendars & Accounts menu. You can track your order by the sample arrival data for a specific run type or email Charlotte for your project ID. Please note that the information on this page reflects sequencing plans for the instruments, but unexpected problems can result in last minute changes.


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