Illumina Sequencing

Illumina NovaSeq, HiSeq, MiSeq and NextSeq

We offer services on Illumina NovaSeq 6000, HiSeq 2000/2500, HiSeq 4000, MiSeq and NextSeq 500. Because of their similar chemistry, same library preparations can be used across these instruments, allowing us to tailor to researchers' sequencing needs according to turn around time (few hours to six-day run) read length (25 bp single-end reads to 300 bp paired-end reads) and throughput (300 Mb/run to 1Tb/run).

Pooling Samples/Barcoding/Indexing Options:
For Illumina sequencing, multiple samples can be pooled into an individual lane/run. Samples may be indexed using Illumina's TruSeq indices, Illumina's Nextera indices or custom indexing adaptors. If the indexing is using the Illumina strategy, the Genomics Facility can separate the reads and provide fastq files for each individual sample.

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Novaseq 6000

Sequencing Output per Flow Cell

 NovaSeq 6000 System
Flow Cell TypeS1S2S4
2 × 50 bp134-167 Gb280–333 GbNA
2 × 100 bp266-333 Gb560–667 GbNA
2 × 150 bp400-500 Gb850–1000 Gb2400-3000 Gb

Specifications based on Illumina PhiX control library at supported cluster densities.
† NA: not applicable

Reads Passing Filter Per Flow Cell

 NovaSeq 6000 System
Flow Cell TypeS1S2S4
Single-end Reads1.3-1.6 B2.8–3.3 B8-10 B
Paired-end Reads2.6-3.2 B5.6–6.6 B16-20 B

Hiseq 4000

Illumina HiSeq 4000 is leveraging innovative patterned flow cell technology to unparalleled speed and performance. HiSeq 4000 delivers the highest throughput and lowest price per sample across multiple applications.

Read lengthRun TimeReads Passing FilterPass Filter Output
Single-end 50 bp< 1 day~330 M/lane~16.5 Gb/lane
Paired-end 2 X 150 bp<3.5 days~660 M/lane~100 Gb/lane
Paired-end 2 x 75 bp**<3 days~660 M/lane~50 Gb/lane

*Specifications based on Illumina PhiX control library. Yield can vary depending on library type. Run times correspond to sequencing only and do not include clustering and primary data processing. Performance may vary based on sample quality, cluster density and other experimental factors.
**Full flowcell only.

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MISEQ

Miseq instrument

Illumina MiSeq is capable of generating approximately 12 million passing filter reads for v2 kits (~24 million for paired-end sequencing) and 22 million for v3 kits (~44 million for paired-end sequencing). The MiSeq desktop sequencer allows you to access more focused applications, such as targeted gene sequencing, metagenomics, small genome sequencing, targeted gene expression or amplicon sequencing. This ability to run long paired-end reads (either 2 x 250 bp or 2 x 300 bp) makes this instrument ideal for amplicon sequencing.

MiSeq Flowcell

MiSeq Standard Runs *

MiSeq v2 kitsRun TimeReads Passing FilterPass Filter Output
Single-end 50 bp~1 day~12 M/run~0.6 Gb/run
Paired-end 2 x 25 bp~1 day~24 M/run~0.6 Gb/run
Paired-end 2 x 150 bp~1.5 days~24 M/run~3.6 Gb/run
Paired-end 2 x 250 bp~2 days~24 M/run~6 Gb/run
MiSeq v3 kits
Single-end 1 x 150 bp~1.5 days~22 M/run~3.3 Gb/run
Paired-end 2 x 75 bp~1.5 days~44 M/run~3.3 Gb/run
Paired-end 2 x 300 bp~3 days~44 M/run~13.2 Gb/run

*Specifications based on Illumina PhiX control library. Yield can vary depending on library type. Run times correspond to sequencing only and do not include primary data processing. Performance may vary based on sample quality, cluster density and other experimental factors.

If you need fewer reads for your project or for testing your library, nano and micro kits are available:

MiSeq Nano and Micro Runs *

Read lengthRun TimeReads Passing FilterPass Filter Output
Paired-end 150 bp Nano~1 day~2 M/run~0.3 Gb/run
Paired-end 250 bp Nano~1 day~2 M/run~0.5 Gb/run
Paired-end 150 bp Micro~1 day~6 M/run~1.2 Gb/run

*Specifications based on Illumina PhiX control library. Yield can vary depending on library type. Run times correspond to sequencing only and do not include primary data processing. Performance may vary based on sample quality, cluster density and other experimental factors.


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Nextseq 500

The NextSeq 500 leverage 2-channel SBS chemistry to offer fast sequencing times for a throughput similar to the HiSeq 4000. The 2-chanel SBS technology requires only two images to determine all four base calls. This results in a two-fold reduction in image acquisition compared to four-channel methods, reducing cycle and data processing times, while delivering the same high quality and accuracy data. Two configurations are available: High throughput and mid-throughput.

High Output Mode*

Read lengthRun TimeClusters Passing FilterPass Filter Output
Single-end 75 bp~11 hours~ 400 M/run~25-30 Gb/run
Paired-end 2 x 75 bp~18 hours~400 M/run~50-60 Gb/run
Paired-end 2 x 150 bp~29 hours~400 M/run~100-120 Gb/run

*Install specifications based on Illumina PhiX control library at supported cluster densities (between 129 and 165 k/mm2 clusters passing filter). Actual performance parameters may vary based on sample type, sample quality and clusters passing filter. All NextSeq 500 kits are paired-end capable.

Mid Output Mode*

Read lengthRun TimeClusters Passing FilterPass Filter Output
Paired-end 2 x 75 bp~ 15 hours~130 M/run~16-19 Gb/run
Paired-end 2 x 150 bp~26 hours~130 M/run~32-39 Gb/run

*Install specifications based on Illumina PhiX control library at supported cluster densities (between 129 and 165 k/mm2 clusters passing filter). Actual performance parameters may vary based on sample type, sample quality and clusters passing filter. All NextSeq 500 kits are paired-end capable.

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