> 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/general/library-preparation-general-reference_material-list/000005679.md).

# Indexed Sequencing workflows with 5' to 3' directionality

**Single-Indexed Sequencing**The single-indexed sequencing workflow applies to all Illumina sequencing platforms, where an Index Read follows Read 1.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-765fa5303630e5c59b88bb8c39e6ed9a64906261%2Fimage1.png?alt=media)

**Dual-Indexed Workflow on a Paired-End Flow Cell**

**Forward Strand Workflow:** MiniSeq with Rapid Reagent kits and the MiSeq.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-daa32a365dd0c94eaeb85b1205c5085add5b61da%2Fimage2.png?alt=media)

**Note**: While MiniSeq Rapid reagents allow for dual indexing, Read 2 cannot be performed with the MiniSeq Rapid reagent kit.

**Reverse Complement Workflow:** iSeq 100, MiSeq i100 Series (read-first sequencing), MiniSeq with Standard reagent kits, NextSeq 500/550, NextSeq 1000/2000, NovaSeq 6000, and NovaSeq X Series.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-1906910a89b6f9c88b4d97311af8e929f1129ec0%2Fimage3.png?alt=media)

For more information, see the [Indexed Sequencing on Illumina Systems Guide](https://support.illumina.com/downloads/indexed-sequencing-overview-15057455.html?langsel=/us/).

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #5679), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005679%20-%20Library%20Preparation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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