Illumina’s Latest Release: HiSeq 3000, 4000, NextSeq 550 and HiSeq X5

HiSeq 3000, HiSeq 4000, HiSeq X Five, HiSeq X Ten

Illumina’s latest instrument release essentially comes down to more data/day.  Using the same patterned flow cell technology already in use with the HiSeq X Ten, The HiSeq 3000 has an output of 750 Gb or 2.5B PE150 reads in 3.5 days. The HiSeq 4000 has two flow cells, so twice the output: 1.5 Tb, 5B PE150 reads in 3.5 days. The NextSeq 550 combines the current NextSeq 500 with a microarray scanning system that fits right into the flow cell holder. The HiSeq X Five is less exciting; just half the number of instruments as the HiSeq X Ten.

If you don’t have the $10M budget for a HiSeq X Ten, you can purchase a HiSeq X Five and scale to the X Ten at a lower price/instrument: $1M/unit

Price Price/unit $/Genome* Consumables $/Gb
HiSeq X Five $6M $1.2M $1,425 $1,200 $10.6
HiSeq X Ten $10M $1M $1,000 $800 $7

*Price per 30X human genome according to Illumina. We’re not aware of any sequencing facility currently offering 30 human genomes for $1,000. On Genohub today, you can order a single whole human genome at 35X for $1,750.

Both the HiSeq X Five and Ten are still only “licensed” for human whole genomes [Update: Since this post was published in January 2015, Illumina now allows the sequencing of other large species on the HiSeq X Ten. For an up to date status on what is and what isn’t allowed on a HiSeq X, follow our HiSeq X Guide Page]. That basically means that while they can technically be used on non-human samples or transcriptomes, Illumina wants these focused on the WGS market (probably thinking about the BGI / Complete Genomic’s WGS instrument release this year).  Plus it gives them an excuse to release patterned flowed cells on more models, hence the HiSeq 3000/4000. Interestingly, Illumina is going to start bundling the TruSeq PCR-free and TruSeq Nano library prep kits (the only chemistry currently compatible with the X Five and X Ten) with X Five/Ten cluster reagents. At least for now, they don’t intend on doing this with the HiSeq series. Other news from this release:

HiSeq 3000/4000 do not have a rapid mode, high-output only. However PE150 reads only take 3.5 days

You can’t upgrade from a HiSeq 2500 (non-patterned flow cell) to a HiSeq 3000 or 4000 (patterned flow cells)

You can upgrade from the single flow cell HiSeq 3000 to dual flow cell HiSeq 4000

HiSeq 3000 yields >200 Gb/day, a 28% increase vs. HiSeq 2500 v4, yet the cost to purchase a HiSeq 3000 is the same as a HiSeq 2500. With two flow cells, the HiSeq 4000 yields twice as much data.

Sequencing Applications and Turnaround Time 

Exomes Transcriptomes 30X Genomes
HiSeq 3000 90 (2×75, <2 days) 50 (2×75, <2 days) 6 (2×150, 3.5 days)
HiSeq 4000 180 (2×75, <2 days) 100 (2×75, <2 days) 12 (2×150, 3.5 days)

So in the end, assuming sequencing facilities aren’t fed up with this break neck upgrade cycle and actually purchase these instruments, researchers can expect more data with faster turnaround times. We’ve already spoken to a few of our service providers who are considering upgrades to their HiSeq 1500/2000 instruments. As soon as these new instruments are available on Genohub, we’ll make an announcement [Update: they are all available, use our NGS Matching Engine for access to the latest Illumina instruments]. If you’d like to be the first to know send us an email at In the meantime, our providers offer services on the HiSeq 2500 v4, HiSeq X Ten, NextSeq 500 and HiSeq instruments (amongst many others).  You can order these services immediately and expect data delivery within the listed guaranteed turn around times. If you’re not sure what technology / instrument is right for you, just enter the number of reads or coverage you need and let our NGS Matching Engine identify the best service for you.  So what’s next? A little bird has told us patterned flow cells on the MiSeq !

2 thoughts on “Illumina’s Latest Release: HiSeq 3000, 4000, NextSeq 550 and HiSeq X5

  1. Are there any publicly available information about prices of Illumina sequencing? I did not found it on Illumina official websie. It is hard to cite a blog, where on price picture is not written even scale of axes.

    Liked by 1 person

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