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Cornell University

NextSeq 500/550 (Illumina) sequencing


The Illumina NextSeq500 instruments are recommended for whole-genome sequencing, exome sequencing, and RNA-Seq experiments. These instruments can process one sample (or pool of samples) on a run.

Depending on the application, the run time, and output per flowcell vary, as indicated in the tables below.

High-output flowcell Reads passing filter* (M/flowcell) Pass filter output (Gbp/flowcell)
75 bp 333-400 25-30
150 bp 333-400 50-60
300 bp 333-400 100-120
Mid-output flowcell Reads passing filter* (M/flowcell) Pass filter output (Gbp/flowcell)
150 bp 130-200 19-30
300 bp 130-200 38-60

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 Illumina 500/550 instruments, 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 500/550 (Illumina) sequencing
DescriptionInternal price (Cornell and Cornell affiliates)External price
High-output kit, 75 bp $1,848 $3,031
High-output kit, 150 bp $3,366 $5,520
High-output kit, 300bp $5,270 $8,643
Mid-output kit, 150 bp $1,166 $1,912
Mid-output kit, 300 bp $1,869 $3,065