# Specifications for the NovaSeq 6000

**Q30 Specifications for v1 vs v1.5 reagent kits**

|            |                                                    |                                           |
| ---------- | -------------------------------------------------- | ----------------------------------------- |
| **Cycles** | **Q30** NovaSeq 6000 **v1**\*\*.0\*\*(SP/S1/S2/S4) | **Q30**NovaSeq 6000 **v1.5**(SP/S1/S2/S4) |
| 1 x 35 bp  | N/A                                                | ≥ 90%                                     |
| 2 × 50 bp  | ≥ 85%                                              | ≥ 90%                                     |
| 2 × 100 bp | ≥ 80%                                              | ≥ 85%                                     |
| 2 × 150 bp | ≥ 75%                                              | ≥ 85%                                     |
| 2 x 250 bp | ≥ 75%                                              | ≥ 75%                                     |

\*\*Performance Parameters for NovaSeq 6000 v1.5 Reagent Kits

Total Expected Output for v1.5 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 supported cluster densities.

**Quality Scores** **for v1.5 Reagent Kits**

|                       |                                              |
| --------------------- | -------------------------------------------- |
| **Run Configuration** | **Quality scores**                           |
| (Kit type)            |                                              |
| 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 v1.5 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, search for Knowledge Base article **Run time estimates for each sequencing step on the Illumina sequencing platform**

**Performance Parameters for NovaSeq 6000 v1.0 Reagent Kits**

**Total Expected Output for v1.0 Reagent Kits**

|                   |                     |
| ----------------- | ------------------- |
| **Output**        | **Flow Cell Types** |
|                   | SP                  |
| 2 × 50 bp         | 65-80 Gb            |
| 2 × 100 bp        | 134-167 Gb          |
| 2 × 150 bp        | 200-250 Gb          |
| 2 × 250 bp        | 325-400 Gb          |
| SR Passing Filter | 650-800 M           |
| PE Passing Filter | 1.3-1.6 B           |

\\\*Specifications based on Illumina PhiX control library at supported cluster densities.

**Quality Scores** **for v1.0 Reagent Kits**

|                       |                                              |
| --------------------- | -------------------------------------------- |
| **Run Configuration** | **Quality scores**                           |
| **(Kit type)**        |                                              |
| 2 × 50 bp             | ≥ 85% of bases higher than Q30 at 2 × 50 bp  |
| 2 × 100 bp            | ≥ 80% of bases higher than Q30 at 2 × 100 bp |
| 2 × 150 bp            | ≥ 75% 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 v1.0 Reagent Kits**

\| Run Time\\\* | SP | S1 | S2 | S4 |\
\| 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, search for Knowledge Base article **Run time estimates for each sequencing step on the Illumina sequencing platform**

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

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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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