> For the complete documentation index, see [llms.txt](https://help.connected.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.connected.illumina.com/dragen-5-base/get-started/readme.md).

# Introduction

### Illumina 5-Base DNA Prep kits support secondary analysis (methylation and variant calling) through DRAGEN Germline, DRAGEN Somatic, and DRAGEN Enrichment. <a href="#pre-sequencing" id="pre-sequencing"></a>

DRAGEN 5-base analysis delivers simultaneous high-accuracy variant calling and single-base-resolution methylation quantification from a single sequencing run, eliminating the need for separate genetic and epigenetic assays. Purpose-built methylation-aware algorithms distinguish true C>T variants from methyl-converted cytosines by leveraging complementary strand information, enabling researchers to uncover both genomic mutations and epigenomic regulation in one streamlined workflow.

DRAGEN Germline, Somatic, and Enrichment support both gDNA and cfDNA inputs. For more information on coverage and sensitivity, please review the [datasheet](https://www.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/illumina-5-base-dna-prep-data-sheet-m-gl-03689/illumina-5-base-dna-prep-data-sheet-m-gl-03689.pdf).

For more information on the value of Illumina 5-base, please read our blog:

1. An introduction to the Illumina 5-Base Solution <https://www.illumina.com/science/genomics-research/articles/5-base-solution.html>
2. From Sample to Insight: Streamlining Analysis with the Illumina 5-Base Solution <https://www.illumina.com/science/genomics-research/articles/from-sample-to-insight-streamlining-analysis-illumina-5-base-solution.html>

### Secondary Analysis

Secondary analysis (alignment to a reference genome, methylation calling, variant calling and annotation, UMIs, and more) may be performed on a local DRAGEN server or in the cloud (BSSH or ICA) using DRAGEN Germline, DRAGEN Somatic, or DRAGEN Enrichment. It is not available on instrument. For these instructions, view the instructions under [Run Analysis Setup](broken://spaces/RW1lxJJB0BWRiV3n2WBc/pages/xUghQ71wUhl65vokz8cj).

It's generally recommended to avoid running DRAGEN Methylation. For more information on this, please review the FAQ on "[How does DRAGEN 5-Base in Germline, Somatic, and Enrichment differ from DRAGEN Methylation?](/dragen-5-base/additional-information/faqs.md)"

For a summary of output files, their sizes, and runtime, please review the FAQs:

* [Output File Overview](/dragen-5-base/additional-information/faqs.md#output-files-summary) and [Presence by Workflow](/dragen-5-base/additional-information/faqs.md#output-file-presence-by-workflow)
* [Approximate Output File Sizes](/dragen-5-base/additional-information/faqs.md#approximate-disk-usage-per-sample)
* [Approximate Runtimes](/dragen-5-base/additional-information/faqs.md#run-time-summary)

Samples may be downsampled; for more information about downsampling, please see <https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/downsampling/fractional-downsampler>.

### Tertiary Analysis

Illumina Connected Multiomics supports post-variant calling analyses, including differential methylation, combining variant regions and differentially methylated regions, and gene set enrichment analysis. For instructions, see the [Connected Multiomics Walkthrough](/dragen-5-base/tertiary-analysis/connected-multiomics-walkthrough.md).


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