# Welcome to DRAGEN Array

DRAGEN (Dynamic Read Analysis for GENomics) Array secondary analysis is a powerful bioinformatics software for Illumina Infinium array-based assays. DRAGEN Array uses cutting-edge data analysis tools to provide accurate, comprehensive, and highly efficient secondary analysis to maximize genomic insights and meet your research needs across multiple applications.

DRAGEN Array is offered as a local package with command-line interface (no specialized server or hardware required) and as a cloud-based package with an intuitive graphical user interface, as summerized in the table below.

<table><thead><tr><th width="188"></th><th width="304">Description</th><th width="353">Key features</th><th>Local analysis</th><th>Cloud analysis</th></tr></thead><tbody><tr><td>Genotyping</td><td>Provides genotyping results for any human Infinium genotyping array.</td><td><ul><li>Greater than 99.5% genotyping accuracy</li><li>Genotyping VCF in as little as 35 seconds per sample</li></ul></td><td><img src="https://2204038178-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FORdIPx9Tl0QxBkTTjyAe%2Fuploads%2Fgit-blob-c901b0b9dc097c99d7e723fa6f91b2eaf77eccc1%2Fcheck.png?alt=media" alt=""></td><td><img src="https://2204038178-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FORdIPx9Tl0QxBkTTjyAe%2Fuploads%2Fgit-blob-c901b0b9dc097c99d7e723fa6f91b2eaf77eccc1%2Fcheck.png?alt=media" alt=""></td></tr><tr><td>PGx – CNV calling</td><td>Provides CNV calling on 7 target PGx genes across 10 target regions, plus genotyping outputs for Infinium microarrays with enhanced PGx content.</td><td><ul><li>Greater than 95% PGx CNV accuracy</li></ul></td><td><img src="https://2204038178-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FORdIPx9Tl0QxBkTTjyAe%2Fuploads%2Fgit-blob-c901b0b9dc097c99d7e723fa6f91b2eaf77eccc1%2Fcheck.png?alt=media" alt=""></td><td><img src="https://2204038178-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FORdIPx9Tl0QxBkTTjyAe%2Fuploads%2Fgit-blob-c901b0b9dc097c99d7e723fa6f91b2eaf77eccc1%2Fcheck.png?alt=media" alt=""></td></tr><tr><td>PGx – star allele annotation</td><td>Provides PGx star allele and variant coverage across 2400+ targets for over 50 genes, plus PGx CNV and genotyping outputs for Infinium microarrays with enhanced PGx content.</td><td><ul><li>Assess hard to discern PGx genes, including the elusive CYP2D6 with greater than 97% call rate</li><li>Obtain all PGx analysis results in ~1 minute per sample</li></ul></td><td><img src="https://2204038178-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FORdIPx9Tl0QxBkTTjyAe%2Fuploads%2Fgit-blob-c901b0b9dc097c99d7e723fa6f91b2eaf77eccc1%2Fcheck.png?alt=media" alt=""></td><td><img src="https://2204038178-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FORdIPx9Tl0QxBkTTjyAe%2Fuploads%2Fgit-blob-c901b0b9dc097c99d7e723fa6f91b2eaf77eccc1%2Fcheck.png?alt=media" alt=""></td></tr><tr><td>Methylation QC</td><td>Provides high-throughput, quantitative methylation quality control for Infinium methylation arrays.</td><td><ul><li>21 algorithm-based quantitative control metrics with adjustable thresholds</li><li>Data summary plots</li><li>Proportion of CG probes passing with user defined p-value threshold</li></ul></td><td></td><td><img src="https://2204038178-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FORdIPx9Tl0QxBkTTjyAe%2Fuploads%2Fgit-blob-c901b0b9dc097c99d7e723fa6f91b2eaf77eccc1%2Fcheck.png?alt=media" alt=""></td></tr><tr><td>Cytogenetics analysis</td><td>Provides cytogenetic CNV calling and LOH (loss of heterozygosity) detection for human Infinium arrays.</td><td><ul><li>Multiple output formats including CNV/LOH VCFs, annotated QC JSONs, and bedgraph files for Log R Ratio and B-Allele Frequency visualization</li><li>Adjustable algorithm thresholds such as minimum deletion, duplication, and LOH sizes and smoothing parameters</li></ul></td><td><img src="https://2204038178-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FORdIPx9Tl0QxBkTTjyAe%2Fuploads%2Fgit-blob-c901b0b9dc097c99d7e723fa6f91b2eaf77eccc1%2Fcheck.png?alt=media" alt=""></td><td><img src="https://2204038178-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FORdIPx9Tl0QxBkTTjyAe%2Fuploads%2Fgit-blob-c901b0b9dc097c99d7e723fa6f91b2eaf77eccc1%2Fcheck.png?alt=media" alt=""></td></tr><tr><td>Cytogenetics analysis + Emedgene interpretation</td><td>Provides cytogenetic CNV calling and LOH (loss of heterozygosity) detection for human Infinium arrays with added visualization and case management in <a href="https://help.emg.illumina.com/">Emedgene</a></td><td><ul><li>Multiple output formats including CNV/LOH VCFs, annotated QC JSONs, and bedgraph files for Log R Ratio and B-Allele Frequency visualization</li><li>Adjustable algorithm thresholds such as minimum deletion, duplication, and LOH sizes and smoothing parameters</li></ul></td><td></td><td><img src="https://2204038178-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FORdIPx9Tl0QxBkTTjyAe%2Fuploads%2Fgit-blob-c901b0b9dc097c99d7e723fa6f91b2eaf77eccc1%2Fcheck.png?alt=media" alt=""></td></tr></tbody></table>

This product documentation describes the installation and setup, analysis execution, and result outputs. For the latest updates and release details, see the [DRAGEN Array Release Notes](https://help.dragenarray.illumina.com/reference/release-notes). See [Introducing DRAGEN™ Array 1.0 for Infinium™ Array-Based Pharmacogenomics Analysis](https://developer.illumina.com/news-updates/introducing-dragen-array-1-0-for-infinium-array-based-pharmacogenomics-analysis) for additional details on DRAGEN Array genotyping, PGx CNV calling and PGx star allele annotation.