NextSeq 2000 Sequencing | University of Minnesota Genomics Center

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The NextSeq 2000 is Illumina’s newest platform that uses advancements in optics, instrument design, and 2-channel chemistry to increase output. This new sequencing technology makes it possible for researchers to sequence a range of conventional and emerging applications by increasing throughput while cutting down on costs per run when compared to its predecessor, the NextSeq 550.

The result is a highly flexible and scalable benchtop system that offers the highest cluster density flow cell of any on-market NGS system to date. It drives down the cost per gigabase making it more accessible for researchers.

As a high-throughout instrument, the NextSeq 2000 is a scalable platform that supports more complex, informative studies and a broad range of standard NGS methods, as well as emerging techniques, including spatialomics. 

This instrument expands the UMGC’s comprehensive sequencing portfolio by replacing the NextSeq 550 as the instrument of choice for projects needing a fast turnaround and increased flexibility.


Currently, there are two types of flow cell options, the P2 and P3, available with a range of outputs to accommodate a wide variety of NGS projects. The P3 is a high-output flow cell that generates up to 1 billion reads per run, more than nearly three times the previously available NextSeq 550.  

The lower-throughput P1 flow cell is expected to be released in the second half of 2021 and will have an output between 20-40 Gb making it an attractive option for MiSeq and NextSeq 550 users. 


The primary advantages of the NextSeq 2000 are the sequencing speed and multiple run configurations that enable sequencing outputs of 36 – 300 Gb per run. 

Four run configurations are available: the 100-cycle kit, the 200-cycle kit, the 300-cycle kit, and the 50-cycle kit, which is available in the P3 only. The added 50-cycle kit targets infectious disease, small RNA, and spatial transcriptomics applications. 

In addition, users have the benefit of not needing to wait to fill a large, multi-lane flow cell (NovaSeq) before data can be generated. Whether it is the P2 or P3 flow cell, researchers purchase the full NextSeq flow cell (no lane splitting) and sequencing will begin once libraries are complete and the instrument is available. 


Due to the 2-channel chemistry, the NextSeq does not tolerate low diversity libraries as well as the MiSeq 4-channel platform, and in order to generate high-quality data, a higher spike-in concentration of a diverse control library is required. Thus, amplicon libraries with low sequence diversity should be designed with phasing bases to frameshift low diversity regions.

In addition, output capacity for custom libraries, including amplicon libraries and low diversity applications, may generate up to 25% less data in an effort to improve data quality. 


Please contact Elyse Cooper or Aaron Becker at for further details on the NextSeq platform.

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