Illumina unveils NovaSeq 5000 and 6000

Illumina NovaSeq

Today, at the annual J.P. Morgan Healthcare Conference, Illumina announced the release of a new series of instruments called NovaSeq. Continuing the use of ExAmp cluster amplification and patterned nano-wells that form the basis of HiSeq 3000/4000 HiSeq X Ten and HiSeq X Five flow cell technology, Illumina further reduced the spacing between nanowells to increase cluster density and data output. In the end, this promises to produce ~ 2-3x more reads than a single 8 lane HiSeq X flow cell.

Here are the specs available on day 1 of launch:

Number of instruments being launched: 2; NovaSeq 5000 and 6000

Non-technical application based restrictions: No, unlike the HiSeq X Ten or HiSeq X Five; these instruments will not have application based restrictions. Illumina plans to continue restricting HiSeq X instruments to WGS applications (1).

Potential technical based restrictions: Notable is the absence of Nextera based DNA or Nextera Exome in the list of compatible library preparation kits. Mate-pair based Nextera kits are however listed as compatible (2). This may indicate there are template (library) size restrictions on this instrument (similar to HiSeq 3000/4000 and HiSeq X).

Instrument availability: NovaSeq 6000 will begin shipping in March 2017 and NovaSeq 5000 will begin shipping mid-2017.

Anticipated availability on GenohubIn April 2017, researchers will be able to order NovaSeq based sequencing. This hinges on on-time instrument delivery to our partnering service providers.

Instrument cost: NovaSeq 5000 and 6000 Systems are priced at $850,000 and $985,000 respectively

Target Market: Research labs that cannot afford the capital cost of a HiSeq X Five or HiSeq X Ten System and don’t want to deal with the restrictions. HiSeq X Five and Ten systems are restricted from running RNA-seq or exome based libraries.

Other updates: RFID added to make sure loading is done properly, reduction in the number of steps in a sequencing workflow (from 38 to 8) (1) and flow cell loading is automated.

Cbot or onboard clustering: onboard

Tunable output: 4 flow cells are available. NovaSeq S1 and S2 flow cells are compatible with both NoveSeq 5000 and 6000 systems while NovaSeq S3 and S4 are exclusive to NovaSeq 6000 instruments.

Two color or Four color chemistry: Two color, like the NextSeq 500

Number of lanes: S1 and S2 have two lanes whereas S3 and S4 have four lanes

Available read lengths: 2×50, 2×100 and 2×150

Run times: < 19, 29 and 40 hours for 2×50, 2×100 and 2×150 bp read lengths respectively


Instrument and flow cell Reads per flow cell *(billion) Output from 2×150 bp run (Gb) *
NovaSeq 5000/6000 S1 1.6 500
NovaSeq 5000/6000 S2 3.3 1000
NovaSeq 6000 S3 6.6 2000
NovaSeq 6000 S4 10 3000

*Output and read numbers based on a single flow cell

Number of flow cells that can be run at once: 1 or 2 flow cells can be run on both the NovaSeq 5000 or 6000

So what does this mean for the sequencing industry? Clearly the Novaseq was launched to target research labs that can’t afford the capital costs of the HiSeq X series but want to upgrade from their current HiSeq instruments. NovaSeq S3 and S4 flow cells promise to produce 2-3x more reads than a single 8 lane HiSeq X flow cell (2.6-3 billion reads).  Of course,  if NovaSeq is priced to run 2-3x more expensive than a HiSeq X flow cell, the cost it takes to sequence a genome will be the same. When reagent pricing is available, this will be more clear.

2016 was a tough year for Illumina as it lost one third of its value. As Illumina launches another instrument geared for the research market, much continues to hinge on federally funded research grants to fuel growth. A focus on developing clinical based applications, insurance reimbursable tests and a global shift toward diagnostics is going to be required for sustained growth. ‘Market generation’ activities, as were initiatives like Helix and Grail are steps in this direction.






2 thoughts on “Illumina unveils NovaSeq 5000 and 6000

  1. Regarding the Nextera Mate-Pair compatibility, note that the kit is so-named because it uses the Nextera tagmentation system to fragment the DNA and add the junction adaptor, however the actual sequencing adaptors are TruSeq chemistry so the limitation may not be library size but chemistry.


  2. A few things:
    So it means that the miSeq becomes the only platform for high quality de novo shotgun/IG amplicon sequencing (requiring 2×250/2×300 reads length) from Illumina once the Hiseq 2500 would be phased out?
    Any plans of having better read quality on a 4 chanel imaging system and supporting at least 2x250bp reads on novaseq (like it was on hiseq 2500)? Can have lower density (biger nanowells) flowcells versions for that (DISCOVAR assembler users would like it).
    Does it use the only the standart P7/P5 adapter sequences during the cluster generation, or it uses longer oligos during cluster generation covering other parts of the sequencing adapter?
    Any info on sensitivity to the short/long libbrary fragments compared to the HiseqX/4000/2500? This may explain the issues with nextera shotgun libraries, which have a wider fragment size distribution compared to covaris fragmentation.
    What is the maximum index length supported?


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