Skip to main content

Cornell University

Illumina sequencing

The Genomics Facility offers several options for Illumina sequencing on different instruments and flowcells (kits) to meet the needs of different research projects.
Coming soon: we will offer services (2x150bp lanes) on NovaSeq6000 and NovaSeq X instruments. These sequencing runs will be sent out to external providers but supported by the Genomics Facility (including local ordering/sample drop-off, QC checks and data management/distribution/archive), and without the need to acquire a quote/PO outside Cornell. Stay tuned for more details coming in mid-February.

General Information

  • Custom sequencing options: We support both custom primers and custom read lengths on all instruments. The number of basepairs listed in the tables below reflect the combined read length per flowcell (kit), and can be configured as single-end or paired-end reads of custom lengths. Contact us prior to placing an order to inquire about customizing your sequencing run.
  • Quality checks: We will assess the concentration and size distribution of your Illumina samples prior to sequencing, and ask you to approve the results before we continue with sequencing. If we observe any problems with sample quality (such as excess primers or adapter dimer peaks), we may recommend additional cleanup steps before sequencing (fees may apply). Samples that do not pass the quality checks will be charged for QC only if sequencing is cancelled.
  • We are available to consult on Illumina sequencing options! Please use the ‘Ask a question’ button at the top of the page to send us an email, or sign up for office hours with an expert.

Instrument Information

This tables below show 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

The MiSeq is a 4-color sequencer ideal for sequencing amplicons or other low complexity samples and for lower output projects

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

NextSeq 500/550

The NextSeq500 is a 2-color sequencer ideal for larger projects with complex libraries. The NextSeqs require the addition of higher amounts of PhiX to enable sequencing of libraries containing low-complexity inserts or read segments.

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

NextSeq 2000

The NextSeq2000 is a 2-color sequencer that uses a patterned flowcell and Illumina’s ExAmp clustering chemistry. Due to the higher frequency of ‘index hopping’ on patterned flowcells, we highly recommend the use of unique dual indices (UDIs) for sample barcoding on this instrument. The P3 flowcell offers the highest output on the NextSeq 2000.

Kit Reads passing filter* (M/flowcell) Pass filter output (Gbp/flowcell)
100 bp (P1) 100 10
300 bp (P1) 100 30
600 bp (P1) 100 60
100 bp (P2) 400 40
200 bp (P2) 400 80
300 bp (P2) 400 120
50 bp (P3) 1100 55
100 bp (P3) 1100 110
200 bp (P3) 1100 220
300 bp (P3) 1100 330

Sample Preparation, Quality Control and Shipping

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 Nano kit, 300 bp (1 M/fc, 0.3 Gbp/run) $445 $655
MiSeq Nano kit, 500 bp (1 M/fc, 0.5 Gbp/run) $525 $785
MiSeq Micro kit, 300 bp (4 M/fc, 1.2 Gbp/run) $650 $990
MiSeq V2 kit, 50 bp (12-15 M/fc, 0.6-0.75 Gbp/run)** $1,285 $2,035
MiSeq V2 kit, 300 bp (12-15 M/fc, 3.6-4.5 Gbp/run)** $1,625 $2,590
MiSeq V2 kit, 500 bp (12-15 M/fc, 7.2-9 Gbp/run) $1,825 $2,920
MiSeq V3 kit, 150 bp (22-25 M/fc, 3.3-3.75 Gbp/run)** $1,410 $2,240
MiSeq V3 kit, 600 bp (22-25 M/fc, 13-15 Gbp/run)** $2,320 $3,370
NextSeq 500/550 High-output kit, 75 bp (333-400 M/fc, 25-30 Gbp/run) $2,355 $3,790
NextSeq 500/550 High-output kit, 150 bp (333-400 M/fc, 50-60 Gbp/run)** $4,255 $6,905
NextSeq 500/550 Mid-output kit, 150 bp (130-200 M/fc, 19-30 Gbp/run) $1,675 $2,675
NextSeq 500/550 High-output kit, 300bp (333-400 M/fc, 100-120 Gbp/run)** $6,635 $10,810
NextSeq 500/550 Mid-output kit, 300 bp (130-200 M/fc, 38-60 Gbp/run)** $2,660 $4,920
NextSeq 2000 P1, 100bp (100 M/fc, 10 Gbp/run)** $2,025 $3,245
NextSeq 2000 P1, 300bp (10 M/fc, 30 Gbp/run)** $2,365 $3,805
NextSeq 2000 P1, 600bp (10 M/fc, 60 Gbp/run)** $2,995 $4,840
NextSeq 2000 P2, 100bp (400 M/fc, 40 Gbp/run) $2,010 $3,225
NextSeq 2000 P2, 200bp (400 M/fc, 80 Gbp/run)** $3,800 $6,160
NextSeq 2000 P2, 300bp (400 M/fc, 120 Gbp/run)** $4,660 $7,570
NextSeq 2000 P3, 100bp (e.g. 2 x 50) (1100 M/fc, 110 Gbp/run)** $4,175 $6,775
NextSeq 2000 P3, 200bp (e.g. 2 x 100) (1100 M/fc, 220 Gbp/run)** $5,625 $9,150
NextSeq 2000 P3, 300bp (e.g. 2 x 150) (1100 M/fc, 330 Gbp/run)** $7,265 $11,840
NextSeq 2000 P3, 50bp (1100 M/fc, 55 Gbp/run)** $3,175 $5,135
M/fc -> Reads passing filter (millions of reads per flowcell - single-end - double for paired-end)
Gbp/run -> Pass filter output (Gbp/run)
Bundled Price includes size QC and ddPCR quantification
**custom order flowcell, longer turnaround
Other Illumina-Related Services
DescriptionInternal price (Cornell and Cornell affiliates)External price
Custom lab work (per hour) $125 $205
Custom data analysis (per hour) $250 $410