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Cornell University

MiSeq (Illumina) sequencing


With its ability to produce long paired-end reads (up to 2 x 300 bp), the Illumina MiSeq instrument is ideal for de novo assembly of small genomes or amplicon sequencing projects.

MiSeq have a single lane per flowcell. These instruments can rapidly run a single sample or pool of samples. Currently, the maximum read length is 300 bp. Depending on the application, the run time ranges from 1 to 2 days.

MiSeq v2 kits Reads passing filter* (M/flowcell) Pass filter output (Gbp/run)
50 bp 12-15 0.6-0.75
300 bp 12-15 3.6-4.5
500 bp 12-15 7.2-9
MiSeq v3 kits Reads passing filter* (M/flowcell) Pass filter output (Gbp/run)
150 bp 22-25 3.3-3.75
600 bp 22-25 13-15
MiSeq Nano kits Reads passing filter* (M/flowcell) Pass filter output (Gbp/run)
300 bp 1 0.3
500 bp 1 0.5
MiSeq Micro kits Reads passing filter* (M/flowcell) Pass filter output (Gbp/run)
300 bp 4 1.2

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 MiSeq instrument, 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

MiSeq (Illumina) sequencing
DescriptionInternal price (Cornell and Cornell affiliates)External price
V2 kit, 50 bp $992 $1,627
V2 kit, 300 bp $1,263 $2,071
V2 kit, 500 bp $1,422 $2,333
V3 kit, 150 bp $1,090 $1,788
V3 kit, 600 bp $1,818 $2,982
Nano kit, 300 bp $321 $527
Nano kit, 500 bp $385 $631
Micro kit, 300 bp $482 $790