DRAGEN
Illumina Connected Software
  • Overview
    • Illumina® DRAGEN™ Secondary Analysis
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    • DRAGEN v4.4
      • Getting Started
      • DRAGEN Host Software
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        • DRAGEN Heme WGS Tumor Only Pipeline
          • Quick Start
          • Sample Sheets
            • Introduction
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              • Custom Workflow
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        • DRAGEN Solid WGS Tumor Normal Pipeline
          • Quick Start
          • Sample Sheets
            • Introduction
            • Requirements
            • Templates
          • Run Planning
            • Sample Sheet Creation in BaseSpace
            • Custom Config Support
          • DRAGEN Server App
            • Quick Start
            • Getting Started
            • Launching Analysis
            • Command Line Options
            • Output
            • Advanced Topics
            • Custom Workflow
              • Custom Config Support
            • Illumina Connected Insights
          • ICA Cloud App
            • Getting Started
            • Launching Analysis
            • Output
            • Advanced Topics
              • Custom Workflow
              • Custom Config Support
              • Post Processing
              • Illumina Connected Insights
          • Analysis Output
          • Analysis Methods
          • Troubleshooting
      • DRAGEN Recipes
        • DNA Germline Panel UMI
        • DNA Germline Panel
        • DNA Germline WES UMI
        • DNA Germline WES
        • DNA Germline WGS UMI
        • DNA Germline WGS
        • DNA Somatic Tumor-Normal Solid Panel UMI
        • DNA Somatic Tumor-Normal Solid Panel
        • DNA Somatic Tumor-Normal Solid WES UMI
        • DNA Somatic Tumor-Normal Solid WES
        • DNA Somatic Tumor-Normal Solid WGS UMI
        • DNA Somatic Tumor-Normal Solid WGS
        • DNA Somatic Tumor-Only Heme WGS
        • DNA Somatic Tumor-Only Solid Panel UMI
        • DNA Somatic Tumor-Only Solid Panel
        • DNA Somatic Tumor-Only Solid WES UMI
        • DNA Somatic Tumor-Only Solid WES
        • DNA Somatic Tumor-Only Solid WGS UMI
        • DNA Somatic Tumor-Only Solid WGS
        • DNA Somatic Tumor-Only ctDNA Panel UMI
        • Illumina scRNA
        • Other scRNA prep
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        • Prepare a Reference Genome
      • DRAGEN DNA Pipeline
        • DNA Mapping
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          • ROH Caller
          • B-Allele Frequency Output
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          • De Novo Small Variant Filtering
          • Autogenerated MD5SUM for VCF Files
          • Force Genotyping
          • Machine Learning for Variant Calling
          • Evidence BAM
          • Mosaic Detection
          • VCF Imputation
          • Multi-Region Joint Detection
        • Copy Number Variant Calling
          • Available pipelines
            • Germline CNV Calling (WGS/WES)
            • Germline CNV Calling ASCN (WGS)
            • Multisample Germline CNV Calling
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            • Somatic CNV Calling WES
            • Somatic CNV Calling ASCN (WES)
          • Additional documentation
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        • Repeat Expansion Detection
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        • Targeted Caller
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        • Structural Variant Calling
          • Structural Variant De Novo Quality Scoring
          • Structural Variant IGV Tutorial
        • VNTR Calling
        • Population Genotyping
        • Filter Duplicate Variants
        • Ploidy Calling
          • Ploidy Estimator
          • Ploidy Caller
        • Multi Caller
        • QC Metrics Reporting
        • JSON Metrics Reporting
        • HLA Typing
        • Biomarkers
          • Tumor Mutational Burden
          • Microsatellite Instability
          • Homologous Recombination Deficiency
          • BRCA Large Genomic Rearrangment
          • DRAGEN Fragmentomics
        • Downsampling
          • Fractional (Raw Reads) Downsampling
        • Unique Molecular Identifiers
        • Indel Re-aligner (Beta)
        • Star Allele Caller
        • High Coverage Analysis
        • CheckFingerprint
        • Population Haplotyping (Beta)
        • DUX4 Rearrangement Caller
      • DRAGEN RNA Pipeline
        • RNA Alignment
        • Gene Fusion Detection
        • Gene Expression Quantification
        • RNA Variant Calling
        • Splice Variant Caller
      • DRAGEN Single Cell Pipeline
        • Illumina PIPseq scRNA
        • Other scRNA Prep
        • scATAC
        • Single-Cell Multiomics
      • DRAGEN Methylation Pipeline
      • DRAGEN MRD Pipeline
      • DRAGEN Amplicon Pipeline
      • Explify Analysis Pipeline
        • Kmer Classifier
        • Kmer Classifier Database Builder
      • BCL conversion
      • Illumina Connected Annotations
      • ORA Compression
      • Command Line Options
        • Docker Requirements
      • DRAGEN Reports
      • Tools and Utilities
    • DRAGEN v4.3
      • Getting Started
      • DRAGEN Host Software
        • DRAGEN Secondary Analysis
      • DRAGEN Reference Support
        • Prepare a Reference Genome
      • DRAGEN DNA Pipeline
        • DNA Mapping
        • Read Trimming
        • DRAGEN FASTQC
        • Sorting and Duplicate Marking
        • Small Variant Calling
          • ROH Caller
          • B-Allele Frequency Output
          • Somatic Mode
          • Joint Analysis
          • De Novo Small Variant Filtering
          • Autogenerated MD5SUM for VCF Files
          • Force Genotyping
          • Machine Learning for Variant Calling
          • Evidence BAM
          • Mosaic Detection
          • VCF Imputation
          • Multi-Region Joint Detection
        • Copy Number Variant Calling
          • CNV Output
          • CNV with SV Support
          • Multisample CNV Calling
          • Somatic CNV Calling WGS
          • Somatic CNV Calling WES
          • Allele Specific CNV for Somatic WES CNV
        • Repeat Expansion Detection
          • De Novo Repeat Expansion Detection
        • Targeted Caller
          • CYPDB6 Caller
          • CYP2D6 Caller
          • CYP21A2 Caller
          • GBA Caller
          • HBA Caller
          • LPA Caller
          • Rh Caller
          • SMN Caller
        • Structural Variant Calling
          • Structural Variant De Novo Quality Scoring
        • VNTR Calling
        • Filter Duplicate Variants
        • Ploidy Calling
          • Ploidy Estimator
          • Ploidy Caller
        • Multi Caller
        • QC Metrics Reporting
        • HLA Typing
        • Biomarkers
          • Tumor Mutational Burden
          • Microsatellite Instability
          • Homologous Recombination Deficiency
          • BRCA Large Genomic Rearrangment
          • DRAGEN Fragmentomics
        • Downsampling
          • Fractional (Raw Reads) Downsampling
          • Effective Coverage Downsampling
        • Unique Molecular Identifiers
        • Indel Re-aligner (Beta)
        • Star Allele Caller
        • High Coverage Analysis
        • CheckFingerprint
        • Population Haplotyping (Beta)
        • DUX4 Rearrangement Caller
      • DRAGEN RNA Pipeline
        • RNA Alignment
        • Gene Fusion Detection
        • Gene Expression Quantification
        • RNA Variant Calling
        • Splice Variant Caller
      • DRAGEN Single-Cell Pipeline
        • scRNA
        • scATAC
        • Single-Cell Multiomics
      • DRAGEN Methylation Pipeline
      • DRAGEN Amplicon Pipeline
      • Explify Analysis Pipeline
        • Kmer Classifier
        • Kmer Classifier Database Builder
      • DRAGEN Recipes
        • DNA Germline Panel UMI
        • DNA Germline Panel
        • DNA Germline WES UMI
        • DNA Germline WES
        • DNA Germline WGS UMI
        • DNA Germline WGS
        • DNA Somatic Tumor-Normal Solid Panel UMI
        • DNA Somatic Tumor-Normal Solid Panel
        • DNA Somatic Tumor-Normal Solid WES UMI
        • DNA Somatic Tumor-Normal Solid WES
        • DNA Somatic Tumor-Normal Solid WGS UMI
        • DNA Somatic Tumor-Normal Solid WGS
        • DNA Somatic Tumor-Only Heme WGS
        • DNA Somatic Tumor-Only Solid Panel UMI
        • DNA Somatic Tumor-Only Solid Panel
        • DNA Somatic Tumor-Only Solid WES UMI
        • DNA Somatic Tumor-Only Solid WES
        • DNA Somatic Tumor-Only Solid WGS UMI
        • DNA Somatic Tumor-Only Solid WGS
        • DNA Somatic Tumor-Only ctDNA Panel UMI
        • RNA Panel
        • RNA WTS
      • BCL conversion
      • Illumina Connected Annotations
      • ORA Compression
      • Command Line Options
      • DRAGEN Reports
      • Tools and Utilities
  • Reference
    • DRAGEN Server
    • DRAGEN Multi-Cloud
      • DRAGEN on AWS
      • DRAGEN on AWS Batch
      • DRAGEN on Microsoft Azure
        • Run DRAGEN VM on Azure
      • DRAGEN on Microsoft Azure Batch
        • Azure Batch Run Modes
    • DRAGEN Licensing
      • DRAGEN Server Licensing
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    • DRAGEN Application Manager
    • Support
    • Resource Files
      • Noise Baselines
    • Supplementary Information
    • Troubleshooting
    • Citing DRAGEN software
    • Release Notes
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  • Installation Procedure on DRAGEN Server
  • Downloader
  • Expected downloaded content
  • Installer
  • Uninstall Heme pipeline

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  1. Product Guides
  2. DRAGEN v4.4
  3. Clinical Research Workflows
  4. DRAGEN Heme WGS Tumor Only Pipeline
  5. DRAGEN Server App

Getting Started

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Last updated 2 days ago

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Installation Procedure on DRAGEN Server

Downloader

A separate lightweight downloader for Windows, MacOS X, and Linux platforms is available at the .

Choose the downloader appropriate for your platform, and follow the download prompts. The required software packages will be downloaded into a designated directory and content that have been previously downloaded is cached to avoid duplication of downloaded content.

If a Windows or MacOS X downloader is chosen, the downloaded directory content may be moved to the installation target DRAGEN server using a USB key with at least 128 GB of free space.

Additional download information is available at the download site.

Expected downloaded content

  • <download_path>/app_installer.run

  • <download_path>/dam_installer.run

  • <download_path>/app_folder/

  • <download_path>/common/

Installer

Installation Requirements

DRAGEN

The Heme Pipeline requires DRAGEN v4.4.4 or higher. If upon installation of the app this version of DRAGEN (or higher) is not installed, the software shall install this version of DRAGEN.

Minimum System Operating Requirements:

Hardware

  • v3 DRAGEN server or v4 DRAGEN server

  • mkfifo is enabled on the network-attached storage (NAS).

Software

The software installed by default on the DRAGEN server includes the following items:

  • DRAGEN server software. Refer to sample sheet settings for the DRAGEN version number.

  • Linux CentOS 7 and Oracle Linux 8 operating systems.

Storage

  • DRAGEN server v3 provides a 6.4 TB NVMe SSD. This SSD is located at the /staging directory and is suitable for storing only one or two runs of the analysis pipeline.

  • DRAGEN server v4 provides 12.8 TB via a 2 x 6.4 TB NVMe U.2 SSD configuration.

  • Consider the following when making data storage decisions.

    • A NovaSeq 6000 sequencing run that uses an S4 flow cell can produce up to 3 TB of output. ▫ The Heme pipeline can produce an additional 4-6 TB of analysis output. For optimal performance when writing to a non-default directory, specify an analysis folder location on /staging, this ensures that the DRAGEN-related processes read and write data to the DRAGEN Server's high-speed NVMe SSD.

    • Network-attached storage is required for long-term storage of sequencing runs and Heme pipeline output.

    • Managing data storage is your responsibility.

      • Illumina recommends developing a strategy to copy data from the DRAGEN server to network-attached storage.

Installation Instructions

  • Installing the Heme pipeline requires root privileges.

    • Follow the instructions for DRAGEN license installation provided by Illumina Customer Care or refer to the DRAGEN server documentation.

  • Store the install_DRAGEN_Heme_WGS-4.4.4.run script in the /staging directory. The script requires approximately 42 GB of free space. An additional 61 GB is needed on /staging if running with TMPDIR=/staging, or on /tmp if running without TMPDIR=/staging. Illumina recommends storing and executing the self-extracting installation script from the /staging directory.

  • Update the permissions on the run script using the following command: • sudo chmod +x /staging/install_DRAGEN_Heme_WGS-4.4.4.run

  • Execute the installation script depending on the targeted software container platform:

    • For Docker, use the following command:

    sudo TMPDIR=/staging /staging/ install_DRAGEN_Heme_WGS-4.4.4.run

Run Self-Test Script

The self-test script, present after app installation, checks the following functions:

  • All required services are running.

  • All resources are in place.

  • The analysis workflow image can be launched.

  • The Heme pipeline can run successfully on a test dataset.

To run the self-test script, execute:

/usr/local/bin/check_DRAGEN_Heme_WGS-4.4.4.sh

If the self-test prints a failure message, contact Illumina Technical Support, and provide the output file found in /staging/check_DRAGEN_Heme_WGS_.tgz.

When running an analysis on the DRAGEN server via SSH, Illumina recommends that you use a terminal multiplexer utility, which allows you to resume analysis in the event of a disconnection from the DRAGEN server.

Uninstall Heme pipeline

To uninstall the Heme pipeline, run the following command as the root user (or with sudo privileges):

/usr/local/bin/uninstall_DRAGEN_Heme_WGS-4.4.4.sh

Executing the uninstall script removes the following assets:

  • All scripts, including:

    • DRAGEN_Heme_WGS-4.4.4.sh

    • check_DRAGEN_Heme_WGS-4.4.4.sh

    • uninstall_DRAGEN_Heme_WGS-4.4.4.sh

    • The resources found in /staging/illumina/DRAGEN_Heme_WGS_4.4.4

    • The dragen_heme_wgs:4.4.4 Docker image.

    You are not required to uninstall DAM, Docker or the DRAGEN server software.

    To remove Docker, review the install instructions for your operating system in the Docker documentation

Delete output data on the DRAGEN server as soon as possible. For additional information on data output and storage, refer to .

Contact Illumina Customer Care to request a link to the Downloader or visit and confirm that the Genome DRAGEN license is enabled for your server.

DRAGEN Installer Download Site
DRAGEN Resource Files
Illumina Instrument Control Computer Security and Networking
DRAGEN Installer Download Site