Illumina NovaSeq, MiSeq and NextSeq
We offer services on Illumina NovaSeq 6000, 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 Sequencing Facility can separate the reads and provide fastq files for each individual sample.
On this Page:
Novaseq 6000
The NovaSeq 6000 is the latest production-scale sequencer from Illumina. The main technical advancements are:
- Patterned flow cells
- 2-color channel chemistry
Additional technical details on the NovaSeq instrument can be found on the Illumina website.
Sequencing Output per Flow Cell
| NovaSeq 6000 System | ||||
|---|---|---|---|---|
| Flow Cell Type | S Prime | S1 | S2 | S4 |
| 2 × 50 bp | 65–80 Gb | 134-167 Gb | 280–333 Gb | NA† |
| 2 × 100 bp | 134–167 Gb | 266-333 Gb | 560–667 Gb | 1600–2000 Gb |
| 2 × 150 bp | 200–250 Gb | 400-500 Gb | 850–1000 Gb | 2400-3000 Gb |
| 2 X 250 bp | 325-400 Gb | NA† | NA† | NA† |
Specifications based on Illumina PhiX control library at supported cluster densities.
† NA: not applicable
Clusters Passing Filter Per Flow Cell
| NovaSeq 6000 System | ||||
|---|---|---|---|---|
| Flow Cell Type | S Prime | S1 | S2 | S4 |
| Clusters* | 650–800 M | 1.3-1.6 B | 3.3-4.1 B | 8-10 B |
* If you are sequencing paired-end, each cluster will generate two reads. If you are sequencing single-end, each cluster will generate one read.
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. 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.