> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/instrumentation/novaseq-6000/instrumentation-novaseq-6000-reference_material-list/000002669.md).

# Specifications for the NovaSeq 6000

\*\*Performance Parameters for NovaSeq 6000 Reagent Kits

Total Expected Output for Reagent Kits\*\*\*

|                            |                     |
| -------------------------- | ------------------- |
| **Output**                 | **Flow Cell Types** |
|                            | **SP**              |
| 1 × 35 bp                  | N/A                 |
| 2 × 50 bp                  | 65-80 Gb            |
| 2 × 100 bp                 | 134-167 Gb          |
| 2 × 150 bp                 | 200-250 Gb          |
| 2 × 250 bp                 | 325-400 Gb          |
| Single read Passing Filter | 650-800 M           |
| Paired-end Passing Filter  | 1.3-1.6 B           |

\*Specifications based on Illumina PhiX control library at recommended loading concentration.

**Quality Scores** **for Reagent Kits**

|                       |                                              |
| --------------------- | -------------------------------------------- |
| **Run Configuration** | **Quality scores**                           |
| (Kit type)            | (SP/S1/S2/S4)                                |
| 1 × 35 bp             | ≥ 90% of bases higher than Q30 at 1 × 35 bp  |
| 2 × 50 bp             | ≥ 90% of bases higher than Q30 at 2 × 50 bp  |
| 2 × 100 bp            | ≥ 85% of bases higher than Q30 at 2 × 100 bp |
| 2 × 150 bp            | ≥ 85% of bases higher than Q30 at 2 × 150 bp |
| 2 x 250 bp            | ≥ 75% of bases higher than Q30 at 2 × 250 bp |

**Run time estimate** **for Reagent Kits**

|                |         |         |         |         |
| -------------- | ------- | ------- | ------- | ------- |
| **Run Time\*** | **SP**  | **S1**  | **S2**  | **S4**  |
| 1 × 35 bp      | N/A     | N/A     | N/A     | \~14 hr |
| 2 × 50 bp      | \~13 hr | \~13 hr | \~16 hr | N/A     |
| 2 × 100 bp     | \~19 hr | \~19 hr | \~25 hr | \~36 hr |
| 2 × 150 bp     | \~25 hr | \~25 hr | \~36 hr | \~44 hr |
| 2 x 250 bp     | \~38 hr | N/A     | N/A     | N/A     |

\***Note**: Run time includes cluster generation, sequencing, and base calling. Run times are based on running 2 flow cells of the same type; starting two different flow cells (lower and higher throughput) will impact run time.

For further information on run time estimates, check Knowledge Base article[Run time estimates for each sequencing step on Illumina sequencing platforms](https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000001540)

See the [NovaSeq 6000 System Specifications page](https://www.illumina.com/systems/sequencing-platforms/novaseq/specifications.html) for more information.

\
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\ <br>

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| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #2669), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002669%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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