DRAGEN
Illumina Connected Software
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        • DNA Germline Panel UMI
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        • DNA Somatic Tumor-Only Solid Panel
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            • Germline CNV Calling (WGS/WES)
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        • Indel Re-aligner (Beta)
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      • DRAGEN RNA Pipeline
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    • 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
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  • Requirements
  • DRAGEN Reports Components
  • Installation
  • Dragen-reports
  • Options
  • Manifests
  • Sample Script
  • Dragen-summary-reports
  • Options
  • Example Script

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  1. Product Guides
  2. DRAGEN v4.4

DRAGEN Reports

DRAGEN Reports are tools for generating rich, interactive and self-contained HTML reports from DRAGEN's output files. These reports combine data from QC, trimming, mapping, variant and other DRAGEN modules to create a comprehensive summary of a multi-sample workflow, as well as more detailed reports for individual samples.

Requirements

The DRAGEN Reports tools are provided as rpm packages. To use it, you will need the following:

  • An x64 processor

  • Red Hat Linux based operating system

In addition, while DRAGEN Reports can accept files output by any DRAGEN process (such as from a local DRAGEN box, DRAGEN equiped sequencing instrument, or the Cloud), it can only work with local files. For how to access your data and transfer it to your local environment, please refer to the user documentation for the appropriate service or instrument.

DRAGEN Reports Components

DRAGEN Reports has two tools for generating different types of report files

  • dragen-reports - Generates reports for a single DRAGEN workflow or pipeline and it's samples

  • dragen-summary-reports - Generate reports for a NovaSeqX run, containing multiple containing multiple DRAGEN workflows

Installation

  1. Download the rpm packages from the Dragen Product Files Support Site

  2. Install dragen-reports by running rpm -i dragen-reports-4.4.4-1.x86_64.rpm

  3. Install dragen-summary-reports by running rpm -i dragen-summary-reports-4.4.4-1.x86_64.rpm

The command line tools are installed at /usr/bin/dragen-reports and /usr/bin/dragen-summary-reports respectively. The data used by the tools are installed at /opt/dragen-reports and /opt/dragen-summary-reports/ respectively.

Dragen-reports

The dragen-reports tool produces both workflow- and sample-level reports. A workflow-level report combines data from multiple samples analyzed by DRAGEN in the same way in order to faciliate comparssions across a batch of samples. Users can navigate to a report for a specific sample by clicking on the link in the Sample column of most workflow report tables.

Sample-level reports are also generated to allowed for more detailed analysis of individual samples. For example, under the DRAGEN-FastQC tab in a workflow report we are only able to plot the mean base quality, while for individual samples we can display a box-and-whisker plot for each position, as shown below.

To navigate back from a sample report to the multi-sample summary, users can click on the "Back to Pipeline" button located in the upper-left corner of the report.

Options

The following command-line options are available from DRAGEN Reports

Option
Argument
Description

-V, --version

Output the version string of the DRAGEN-Reports executable

-v, --verbose

Emit additional debug information whiile generating the report

-m, --manifest

Filepath

Specify a manifest file describing the report to be written

-n, --run-name

String

Manually set the run-name in the output report

-d, --directory

Comma-separated list

DRAGEN output directories to generate a report from

-o, --output

Filepath

Generate output report to the specified location

-s, --samples

Comma-separated list

Generate only individual reports for the specified sample(s)

-S, --sample-output

Filepath

Generate sample report to the specified location

-f, --force

Force overwriting of any pre-existing report files

-T, --timestamp

String

Manually set the timestamps in the output reports

-h, --help

Display this help command

Manifests

The dragen-reports tool can output reports with different contents for different DRAGEN workflows, tailoring the resulting reports to create only the most relevant plots and tables. To utilize this feature, users can use the -m / --manifest option to specify a Manifest JSON file to specify the desired output reports. These files function as recipes for different reports - specifying which files to look for, which data to process, and which plots to draw. These files are all available in the DRAGEN Reports docker under the /opt/dragen-reports/manifests directory.

Manifest
Name
Pipeline
Description

germline_wgs.json

Germline Report

DragenGermline

Default manifest targetting WGS workflows and supporting most DRAGEN variant callers

somatic_wgs.json

Somatic Report

DragenSomatic

Manifest for somatic tumor-only analysis

germline_enrichment.json

Enrichment Report

DragenEnrichment

Manifest for whole exome or germline gene panel analysis

somatic_enrichment.json

Enrichment Report

DragenEnrichment

Manifest for somatic exomes or somatic gene panel analysis

rna.json

RNA Report

DragenRna

Manifest for RNA-Seq & RNA Quantification workflows

methylation.json

Methylation Report

DragenMethylation

Manifest for the DRAGEN Methylation workflow

demux.json

Demultiplex Report

Demux

Manifest for DRAGEN demultiplex processes

bcl_convert.json

BCL Convert Report

BCLConvert

Manifest for BCLConvert and library QC workflows

Sample Script

Below is a sample Bash script for running the dragen-reports command line tool, with a line-by-line explanation

1    /usr/bin/dragen-reports \
2      -f \
3      -d /data \
4      -o /output/report.html
5      -m /opt/dragen-reports/manifests/germline_wgs.json
  1. Call to execute the dragen-reports command-line tool

  2. --force option, to enable over-writing of any pre-existing output files

  3. --directory option specifying the input data directory

  4. --output option specifying the report file to output

  5. --manifest option to specify the manifest file to use - in this case we are requesting a WGS Germline report

Dragen-summary-reports

The dragen-summary-reports tool produces reports for DRAGEN analysis results from a NovaSeqX instrument. These reports summarize which DRAGEN workflows were run, which version of DRAGEN was used, which sample project they belonged to (if any), and how many samples and errors there were. If a workflow-level report is available for a given workflow, such as one generated by dragen-reports, that report will be linked from the Workflow column. In addition sub-reports are created for any sample projects, containing the subset of data for that specific project, and linked from the Sample Project column.

Options

The following command-line options are available from DRAGEN Summary Reports

Option
Argument
Description

-V, --version

Output the version string of the DRAGEN-Reports executable

-v, --verbose

Emit additional debug information whiile generating the report written

-n, --run-name

String

Manually set the run-name in the output report

-d, --directory

Directory path

DRAGEN output directories to generate a report from

-o, --output

Filepath

Generate output report to the specified location

-f, --force

Force overwriting of any pre-existing report files

-h, --help

Display this help command

Example Script

1    /usr/bin/dragen-summary-reports \
2      -f \
3      -d /data \
4      -o /data/AggregateReports/summary.html
  1. Call to execute the dragen-summary-reports command-line tool

  2. --force option, to enable over-writing of any pre-existing output files

  3. --directory option specifying the input data directory

  4. --output option specifying the report file to output

NOTE Due to the fact that dragen-summary-reports makes extensive use of symbolic links to prevent the duplication of large report files, the --directory and --output arguments must point to the same mounted volume

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