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.
We now offer services (2x150bp lanes) on NovaSeq instruments. These sequencing runs are 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. 

General Information

  • Selecting an Illumina instrument and sequencing kit to fit your project needs: there are important differences in read lengths, output, sequencing chemistry, and ability to customize the run. See below for technical details about each Illumina instrument and run type.
  • Sequencing output is shown for typical runs, but performance may vary, particularly for libraries with any regions of low complexity or for non-standard library types. Typical yields (Reads passing filter* values) represent the number of clusters sequenced; given for single-end (SE) reads. Paired-end (PE) mode generates twice as many reads as single-end mode for the same number of clusters.
  • Custom sequencing options: We support both custom primers and custom read lengths on the MiSeq, NextSeq500, and NextSeq2000 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. Sequencing runs on the NovaSeq instruments are standardized to 2x150bp paired-end (PE) reads, with limited options for index read lengths and no custom sequencing primers. Contact us prior to placing an order to discuss options.
  • Sequencing chemistry: Illumina’s new XLEAP chemistry used on the 2-color NovaSeqX and NextSeq2000 instruments has important implications for color balancing of the index reads, especially for sequencing runs containing a small number of libraries (low diversity index reads). Each position in the index read should generate signal in both channels to minimize issues with sequencing quality. With XLEAP chemistry, ‘C’ is the dual color nucleotide that generates signal in both channels; with Illumina’s older standard Sequencing By Synthesis (SBS) chemistry used on the NextSeq500 (and optionally the NextSeq2000), ‘A’ is the dual color nucleotide. ‘G’ generates no signal for both chemistries, and the other 2 bases generate signal in 1 channel. If you use an instrument+flowcell with XLEAP chemistry, please plan for this change in index color balancing when barcoding your libraries. (Note that the miSeq is a 4-color sequencer and index color balancing is rarely a concern.)
  • Quality checks: We will assess the concentration and size distribution of your Illumina samples and will ask you to approve the results before we continue with the sequencing run. 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

NovaSeq instruments

The NovaSeqX is a 2-color sequencer that uses a patterned flowcell and Illumina’s new XLEAP 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. We offer sequencing lanes on the 10B and 25B 8-lane flowcells with 2 x 150bp paired end reads as the standard format on this instrument, with limited options for index read lengths. New: for projects requiring less than a full lane of sequencing, we now support lane sharing on the NovaSeq platform (2x150nt PE reads, max 10nt index read lengths, UDIs required). Other flowcells and sequencing read lengths may be available by special order and potentially only for the entire flowcell (8 lanes); contact us for more information. We can also provide sequencing options on the older NovaSeq6000 instrument (standard SBS chemistry), either individual lanes on the P4 flowcell (2x150nt PE reads) or full flowcells (2-4 lanes) with custom read lengths by special order.

KitReads passing filter* (M/flowcell)Pass filter output (Gbp/run)
NovaSeqX-10B 300 bp (10B) - 1 lane1100-1250330-375
NovaSeqX-25B 300 bp (25B) - 1 lane3000-3300900-1000
NovaSeq6000-S4 300 bp - 1 lane2000-2500600-750

NextSeq 2000

The NextSeq2000 is a 2-color sequencer that uses a patterned flowcell and Illumina’s standard SBS 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. Flowcells are now available for both XLEAP and standard SBS chemistry; XLEAP flowcells are often less expensive than standard SBS. See above for notes on differences in index color balancing between XLEAP and standard SBS. The new P4 flowcell (XLEAP chemistry only) offers the highest output on the NextSeq 2000.

KitReads passing filter* (M/flowcell)Pass filter output (Gbp/flowcell)
P1-100 bp10010
P1-300 bp 10030
P1-600 bp10060
P2-100 bp40040
P2-200 bp40080
P2-300 bp400120
P3-50 bp (standard SBS only)110055
P3-100 bp1100110
P3-200 bp1100220
P3-300 bp1100330
P4-50 bp (XLEAP only)170085
P4-100 bp (XLEAP only)1700170
P4-200 bp (XLEAP only)1700340
P4-300 bp (XLEAP only)1700510

NextSeq 500/550

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

KitReads passing filter* (M/flowcell)Pass filter output (Gbp/flowcell)
75 bp (High-output)333-40025-30
150 bp (High-output)333-40050-60
300 bp (High-output)333-400100-120
150 bp (Mid-output)100-13019-30
300 bp (Mid-output)100-13038-60

MiSeq

The MiSeq is a 4-color sequencer ideal for sequencing amplicons or other low complexity samples and for lower output projects. Low complexity pools will have lower data output due to increased % PhiX and lower loading density requirements. Contact us to consult on optimizing amplicon sequencing to improve data quality and output. 

KitReads passing filter* (M/flowcell)Pass filter output (Gbp/run)
50 bp (v2)12-150.6-0.75
300 bp (v2)12-153.6-4.5
500 bp (v2)12-157.2-9
150 bp (v3)22-253.3-3.75
600 bp (v3)22-2513-15
300 bp (nano)10.3
500 bp (nano)10.5
300 bp (micro)41.2

Illumina sample preparation and shipping

Service pricing

Illumina sequencing (stocked flowcells)
DescriptionInternal price (Cornell and Cornell affiliates)External price
MiSeq Nano kit, 300 bp (1 M/fc, 0.3 Gbp/run) $445 $730
MiSeq Nano kit, 500 bp (1 M/fc, 0.5 Gbp/run) $525 $860
MiSeq Micro kit, 300 bp (4 M/fc, 1.2 Gbp/run) $650 $1065
MiSeq V2 kit, 500 bp (12-15 M/fc, 7.2-9 Gbp/run) $1,825 $2,995
NextSeq 500/550 High-output kit, 75 bp (333-400 M/fc, 25-30 Gbp/run) $2,355 $3,865
NextSeq 500/550 Mid-output kit, 150 bp (100-130 M/fc, 19-30 Gbp/run) $1,675 $2,750
NextSeq 2000 P2, 100bp (400 M/fc, 40 Gbp/run) $2,010 $3,300
NovaSeq6000 S4 flowcell (1 lane), 2x150bp (2000 M/lane, 600 Gbp/lane) $5,015 $8,225
NovaSeqX 10B flowcell (1 lane), 2x150bp (1100 M/lane, 330 Gbp/lane) $1,735 $2,845
NovaSeqX 25B flowcell (1 lane), 2x150bp (3000 M/lane, 900 Gbp/lane) $2,995 $4,910
NovaSeqX shared lane, first 50M reads $200 $330
NovaSeqX shared lane, additional 50M reads $100 $165
M/fc -> Reads passing filter (millions of reads per flowcell - single-end - double for paired-end)
Gbp/run -> Pass filter output (Gbp/run)
Illumina sequencing (custom order flowcell, longer turnaround)
DescriptionInternal price (Cornell and Cornell affiliates)External price
MiSeq V2 kit, 50 bp (12-15 M/fc, 0.6-0.75 Gbp/run) $1,285 $2,110
MiSeq V2 kit, 300 bp (12-15 M/fc, 3.6-4.5 Gbp/run) $1,625 $2,665
MiSeq V3 kit, 150 bp (22-25 M/fc, 3.3-3.75 Gbp/run) $1,410 $2,315
MiSeq V3 kit, 600 bp (22-25 M/fc, 13-15 Gbp/run) $2,320 $3,805
NextSeq 500/550 High-output kit, 150 bp (333-400 M/fc, 50-60 Gbp/run) $4,255 $6,980
NextSeq 500/550 High-output kit, 300bp (333-400 M/fc, 100-120 Gbp/run) $6,635 $10,885
NextSeq 500/550 Mid-output kit, 300 bp (100-130 M/fc, 38-60 Gbp/run) $2,660 $4,365
NextSeq 2000 P1, 100bp (100 M/fc, 10 Gbp/run) $1,975 $3,240
NextSeq 2000 P1, 300bp (100 M/fc, 30 Gbp/run) $2,245 $3,685
NextSeq 2000 P1, 600bp (100 M/fc, 60 Gbp/run) $2,550 $4,185
NextSeq 2000 P2, 200bp (400 M/fc, 80 Gbp/run) $3,040 $4,985
NextSeq 2000 P2, 300bp (400 M/fc, 120 Gbp/run) $3,445 $5,650
NextSeq 2000 P2, 600bp (400 M/fc, 240 Gbp/run) $4,520 $7415
NextSeq 2000 P3, 50bp (1100 M/fc, 55 Gbp/run) **XLEAP not available $3,175 $5,210
NextSeq 2000 P3, 100bp (e.g. 2 x 50) (1100 M/fc, 110 Gbp/run) $3,420 $5,610
NextSeq 2000 P3, 200bp (e.g. 2 x 100) (1100 M/fc, 220 Gbp/run) $4,465 $7,325
NextSeq 2000 P3, 300bp (e.g. 2 x 150) (1100 M/fc, 330 Gbp/run) $5,155 $8,455
NextSeq 2000 P4, 50bp (1700 M/fc, 85 Gbp/run) $3,285 $5,390
NextSeq 2000 P4, 100bp (e.g. 2 x 50) (1700 M/fc, 170 Gbp/run) $4,040 $6,625
NextSeq 2000 P4, 200bp (e.g. 2 x 100) (1700 M/fc, 340 Gbp/run) $5,365 $8,800
NextSeq 2000 P4, 300bp (e.g. 2 x 150) (1700 M/fc, 510 Gbp/run) $6,110 $10,020
NovaSeqX and NovaSeq 6000 services using flowcells/run types not listed above Inquire Inquire
For Nextseq 2000 flowcells, pricing is shown for new XLEAP chemistry; flowcells using the standard SBS chemistry can be ordered, however the price is often higher (please inquire). Info Info
M/fc -> Reads passing filter (millions of reads per flowcell - single-end - double for paired-end)
Gbp/run -> Pass filter output (Gbp/run)
Other Illumina-Related Services
DescriptionInternal price (Cornell and Cornell affiliates)External price
Custom lab work (per hour) $55 $90
Consultation and custom data analysis (per hour) $125 $205