> For the complete documentation index, see [llms.txt](https://help.dragen.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-single-cell-pipeline.md).

# DRAGEN Single Cell Pipeline

DRAGEN v4.5 provides support for the Illumina Single Cell 3' RNA Prep library based on PIPseq technology.\
[DRAGEN scRNA Illumina Prep User Guide](/dragen-v4.5/product-guides/dragen-v4.5/dragen-single-cell-pipeline/dragen-scrna-illumina.md)

DRAGEN also supports analysis of non-Illumina prep single cell samples.\
[DRAGEN scRNA Other Prep User Guide](/dragen-v4.5/product-guides/dragen-v4.5/dragen-single-cell-pipeline/dragen-scrna-other.md)

DRAGEN supports single cell ATAC-seq analysis as well.\
[DRAGEN scATAC User Guide](/dragen-v4.5/product-guides/dragen-v4.5/dragen-single-cell-pipeline/dragen-scatac.md)

Finally, DRAGEN supports dual analysis of matched scRNA and scATAC samples, referred to as "DRAGEN Single Cell Multiomics".\
[DRAGEN Single Cell Multiomics User Guide](/dragen-v4.5/product-guides/dragen-v4.5/dragen-single-cell-pipeline/dragen-multiomics.md)

(Note that DRAGEN Single Cell Multiomics has not yet been tested with Illumina scRNA prep.)


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