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Cornell University

Illumina sequencing

MiSeq

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.

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.

NextSeq 500/550

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.

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.

NextSeq 2000

  • 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.

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.

Run Types

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.

MiSeq

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

NextSeq 500/550

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

NextSeq 2000

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

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

Illumina sequencing
DescriptionInternal price (Cornell and Cornell affiliates)External price
MiSeq V2 kit, 50 bp (12-15 M/fc, 0.6-0.75 Gbp/run) $992 $1,627
MiSeq V2 kit, 300 bp (12-15 M/fc, 3.6-4.5 Gbp/run) $1,263 $2,071
MiSeq V2 kit, 500 bp (12-15 M/fc, 7.2-9 Gbp/run) $1,422 $2,333
MiSeq V3 kit, 150 bp (22-25 M/fc, 3.3-3.75 Gbp/run) $1,090 $1,788
MiSeq V3 kit, 600 bp (22-25 M/fc, 13-15 Gbp/run) $1,818 $2,982
MiSeq Nano kit, 300 bp (1 M/fc, 0.3 Gbp/run) $321 $527
MiSeq Nano kit, 500 bp (1 M/fc, 0.5 Gbp/run) $385 $631
MiSeq Micro kit, 300 bp (4 M/fc, 1.2 Gbp/run) $482 $790
NextSeq 500/550 High-output kit, 75 bp (333-400 M/fc, 25-30 Gbp/run) $1,848 $3,031
NextSeq 500/550 High-output kit, 150 bp (333-400 M/fc, 50-60 Gbp/run) $3,366 $5,520
NextSeq 500/550 High-output kit, 300bp (333-400 M/fc, 100-120 Gbp/run) $5,270 $8,643
NextSeq 500/550 Mid-output kit, 150 bp (130-200 M/fc, 19-30 Gbp/run) $1,166 $1,912
NextSeq 500/550 Mid-output kit, 300 bp (130-200 M/fc, 38-60 Gbp/run) $1,869 $3,065
NextSeq 2000 P2, 100bp (400 M/fc, 40 Gbp/run) $1,787 $2,931
NextSeq 2000 P2, 200bp (400 M/fc, 80 Gbp/run) $3,360 $5,510
NextSeq 2000 P2, 300bp (400 M/fc, 120 Gbp/run) $4,455 $7,306
NextSeq 2000 P3, 50bp (1100 M/fc, 55 Gbp/run) $2,723 $4,466
NextSeq 2000 P3, 100bp (e.g. 2 x 50) (1100 M/fc, 110 Gbp/run) $3,933 $6,450
NextSeq 2000 P3, 200bp (e.g. 2 x 100) (1100 M/fc, 220 Gbp/run) $5,445 $8,930
NextSeq 2000 P3, 300bp (e.g. 2 x 150) (1100 M/fc, 330 Gbp/run) $7,260 $11,906
M/fc -> Reads passing filter (millions of reads per flowcell - single-end - double for paired-end)
Gbp/run -> Pass filter output (Gbp/run)