> 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/library-preparation/custom-third-party-library-prep/library-preparation-custom-third-party-library-prep-reference_material-list/000001478.md).

# Considerations when migrating non-Illumina libraries between sequencing platforms

Sequencing libraries prepared with non-Illumina library preparation methods or kits may require additional optimization on different sequencing platforms. Consider the following differences:

**The iSeq 100, MiniSeq, MiSeq, MiSeq i100 Series, NextSeq 500/550, NextSeq 1000/2000, NovaSeq 6000, and NovaSeq X Series flow cells are paired-end flow cells.**

* Note: single read sequencing can be performed on these platforms, but paired end type flow cells are a specific flow cell design, distinct from single read flow cell types.

Libraries with paired-end adapter designs can be run as single-read or paired-end sequencing runs, but some older single-read libraries may not sequence successfully on modern paired-end flow cells. As a result, it may not be possible to successfully sequence some libraries developed for single-read applications on the HiSeq 1000/1500/2000/2500 instruments on current sequencing platforms.

For guidance on if a library has a single-read or paired-end adapter design, contact [Illumina Technical Support](https://www.illumina.com/company/contact-us.html).

**Primer Binding and SBS chemistry temperatures**

Temperatures used for primer binding, deblocking, and nucleotide incorporation steps can vary between platforms and therefore need to be considered when using custom sequencing primers or primer binding sites.

| **Platform**          | **Primer Binding** | **Deblocking** | **Incorporation** |
| --------------------- | ------------------ | -------------- | ----------------- |
| **iSeq 100**          | 65° C              | 63° C          | 65° C             |
| **MiniSeq**           | 60° C              | 60° C          | 60° C             |
| **MiSeq**             | 65° C              | 60° C          | 65° C             |
| **MiSeq i100 Series** | 65° C              | 56° C          | 65° C             |
| **NextSeq 500/550**   | 60° C              | 60° C          | 60° C             |
| **NextSeq 1000/2000** | 60° C              | 60° C          | 60° C             |
| **NovaSeq 6000**      | 60° C              | 55° C          | 60° C             |
| **NovaSeq X Series**  | 60° C              | 60° C          | 60° C             |

**Clustering efficiency**

Libraries can exhibit different clustering efficiencies when migrating from one platform to another. See [Loading concentration considerations when migrating Illumina libraries between sequencing platforms](/instrumentation/general/instrumentation-general-reference_material-list/000001509.md) for additional information on these variations.

**Additional considerations**

* Insert sizes more than 550 bp are generally not supported on the MiniSeq or NextSeq 500/550,and may require additional optimization steps.
* Some applications with 550 bp or greater insert sizes are compatible with the NovaSeq 6000 platform, but additional optimization steps may be required.
* Sequencing low diversity libraries can require additional optimization across different instruments.

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #1478), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001478%20-%20Library%20Preparation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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