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Cornell University

NextSeq 2000 (Illumina) sequencing

The Illumina NextSeq 2000 (or 2k as we call it in house) is the most cost-effective sequencing platform currently in the Genomics Core.


  • The NextSeq 2k uses patterned flowcells and Illumina’s ExAmp clustering chemistry, which require more stringent quality control prior to sequencing libraries.
  • We also recommend using UDI (unique dual indexing) when prepping samples to be sequenced on this instrument. UDI is a known mitigation for filtering index-hopped reads seen in downstream analyses.
  • Illumina’s P2 flowcells produce a similar number of reads when compared with NextSeq 500/550 flowcells, but the smallest kit available for the P2 is 100 bp (vs. 75 bp for the NextSeq 500/550), which may be attractive for certain applications.

  • Illumina’s P3 flowcells have sequencing lanes that are physically larger than the P2 flowcells. This allows P3 flowcells to output around 1 billion fragments sequenced, or ~2.5 times the output of a NextSeq 2k or a NextSeq 500/550 flowcell.

P2 kits Reads passing filter* (M/flowcell) Pass filter output (Gbp/flowcell)
100 bp 400 40
200 bp 400 80
300 bp 400 120
P3 kits Reads passing filter* (M/flowcell) Pass filter output (Gbp/flowcell)
50 bp 1100 55
100 bp 1100 110
200 bp 1100 220
300 bp 1100 330

This table shows nominal read lengths. Different length runs can be performed, depending on the type of sample/indexing used. Contact us prior to placing an order to discuss options.
* Values given for single-end reads. Paired-end mode would generate twice as many reads.


We provide a variety of read length options, as reflected in our price list. With the NextSeq 2k, runs can be configured with some flexibility. For example, a 50 bp kit can be used for a paired-end 2 x 25 bp run. In some cases, we may be able to offer custom read lengths. Please contact us to discuss options for your project.

Don't overpay for bad samples

If the QC results for the samples indicate poor quality and sequencing is not recommended, we will not process your samples. You will be charged only for the QC, not the sequencing of samples that are likely to fail.

Illumina sample preparation and shipping

Service pricing

NextSeq 2000 (Illumina) sequencing
DescriptionInternal price (Cornell and Cornell affiliates)External price
P2 100bp Cycles $1,787 $2,931
P2 200bp Cycles $3,360 $5,510
P2 300bp Cycles $4,455 $7,306
P3 50bp Cycles $2,723 $4,466
P3 100bp Cycles (e.g. 2 x 50) $3,933 $6,450
P3 200bp Cycles (e.g. 2 x 100) $5,445 $8,930
P3 300bp Cycles (e.g. 2 x 150) $7,260 $11,906