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 Type | S1 | S2 | S4 |
| 2 × 50 bp | 134-167 Gb | 280–333 Gb | NA† |
| 2 × 100 bp | 266-333 Gb | 560–667 Gb | NA† |
| 2 × 150 bp | 400-500 Gb | 850–1000 Gb | 2400-3000 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 Type | S1 | S2 | S4 |
| Single-end Reads | 1.3-1.6 B | 2.8–3.3 B | 8-10 B |
| Paired-end Reads | 2.6-3.2 B | 5.6–6.6 B | 16-20 B |
The Illumina HiSeq 2000/2500 instrument is a high-throughput sequencer that supports a wide spectrum of applications and projects of various sizes. This instrument can operate in two modes: High Output Mode (eight-lane flowcell) and Rapid Mode (two-lane flowcell).
 |  |
| High Output Mode HiSeq Flowcell | Rapid Mode HiSeq Flowcell |
High output mode
Our instruments are upgraded to the HiSeq v4 chemistry and are capable of generating up to 250 million reads per land passing filter or up to 500 million reads passing filter for paired-end sequencing. In high output mode this instrument is only available for full flow cells requests (8 lanes). Read lengths available are single-end 50bp, single-end 100 bp, paired-end 2 x 50 bp, paired-end 2 x 125 bp, and paired-end 2 x 100 bp.
If faster turnaround times are needed, consider performing a "Rapid Run."
HiSeq High Output Mode, v4 chemistry *
| Read length | Run Time | Reads Passing Filter | Pass Filter Output |
|---|---|---|---|
| Single-end 50 bp | ~2 day | ~250 M/lane | ~12.5 Gb/lane |
| Paired-end 2 x 125 bp | ~6 days | ~500 M/lane | ~62.5 Gb/lane |
| Single-end 100 bp ** | ~3.5 day | ~250 M/lane | ~25 Gb/lane |
| Paired-end 2 x 50 bp ** | ~3.5 days | ~500 M/lane | ~25 Gb/lane |
| Paired-end 2 x 100 bp ** | ~5 days | ~500 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.
Rapid Mode
In "Rapid Run Mode," the Illumina HiSeq 2500 instrument is capable of generating approximately 150 millions reads passing filter per lane, or up to 300 million reads passing filter per lane for paired-end sequencing. This is a two-lane flowcell. Because clustering happens on-board, both lanes are loaded with the same library pool. Alternative loading with two independent lanes is available upon request with additional cost.
HiSeq High Rapid Mode *
| Read length | Run Time | Reads Passing Filter | Pass Filter Output |
|---|---|---|---|
| Single-end 50 bp | ~1 day | ~300 M/run | ~15 Gb/lane |
| Paired-end 25 bp | ~1 day | ~600 M/run | ~15 Gb/lane |
| Single-end 100 bp | ~1.5 days | ~300 M/run | ~30 Gb/run |
| Paired-end 2 x 100 bp | ~2 days | ~600 M/run | ~60 Gb/run |
| Paired-end 2 x 150 bp | ~2.5 days | ~600 M/run | ~90 Gb/run |
| Paired-end 2 x 250 bp | ~3 days | ~600 M/run | ~150 Gb/run |
*Specifations 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.
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 length | Run Time | Reads Passing Filter | Pass 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.
MISEQ
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 kits | Run Time | Reads Passing Filter | Pass 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 length | Run Time | Reads Passing Filter | Pass 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.
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 length | Run Time | Clusters Passing Filter | Pass 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 length | Run Time | Clusters Passing Filter | Pass 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.