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.
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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.
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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.
Service pricing
Description | Internal 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) |