Illumina DRAGEN

https://help.dragen.illumina.com
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Illumina DRAGEN is a secondary analysis platform for processing Next Generation Sequencing (NGS)...
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### Run Dragen Analysis on Local Server (BCL Input)

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/quick-start

This snippet shows how to initiate a Dragen analysis on a local server starting from BCL files. It requires specifying the input and output folders. Use '--help' for a full list of parameters.

```bash
<pipeline_run_script> --help # list all supported parameters
<pipeline_run_script> --inputType bcl \
--inputFolder /staging/input-folder \
--analysisFolder /staging/output-folder
```

--------------------------------

### Install DRAGEN License from File (Offline)

Source: https://help.dragen.illumina.com/reference/licensing/onprem_licensing

This command installs a DRAGEN license from a specified binary file (.bin). This method is primarily intended for dark site (offline) systems where automatic retrieval is not possible. Each license file must be installed individually.

```bash
sudo dragen_lic -i <license file received>.bin
```

```bash
sudo dragen_lic -i license_genome.bin
```

```bash
sudo dragen_lic -i license_compression.bin
```

```bash
sudo dragen_lic -i license_cnv.bin
```

```bash
sudo dragen_lic -i license_somatic.bin
```

```bash
sudo dragen_lic -i license_transcriptome.bin
```

```bash
sudo dragen_lic -i license_jointgenotype.bin
```

--------------------------------

### Install Heme Pipeline

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation

Launches the Heme pipeline installer with root privileges. This command initiates the installation process on the DRAGEN server.

```shell
sudo /path/to/install_Heme_WGS_TO_v{version}.run
```

--------------------------------

### Launch DRAGEN Pipeline Installer

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation

Executes the DRAGEN pipeline installer with root privileges. This command initiates the installation process on the target server.

```shell
sudo /path/to/install_Solid_WGS_TN_v{version}.run
```

--------------------------------

### FASTQ File Entry Example

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/bcl-conversion

An example of a complete FASTQ file entry, illustrating the format of read identifiers and quality scores. This format can be modified by specific DRAGEN options.

```text
`@SIM:1:FCX:1:2106:15337:1063:GATCTGTACGTC 1:N:0:ATCACGGATCTGTACGTCTCTGCNTCACCTCCACCGTGCAACTCATCACGCAGCTCATGCCCTTCGGCTGCCTCCTGGACTA + CCCCCGGGGGGGGGGGG#:CFFGFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGFGGG`
```

--------------------------------

### Run Dragen Analysis on Local Server (FASTQ, BAM, CRAM Input)

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/quick-start

This command demonstrates running a Dragen analysis on a local server with FASTQ, BAM, or CRAM files. It supports specifying multiple input folders separated by commas.

```bash
<pipeline_run_script> --inputType <fastq|bam|cram> \
--inputFolder /staging/input-folder-1,/staging/input-folder-2 \
--analysisFolder /staging/output-folder
```

--------------------------------

### Get Application-Specific Help (Shell)

Source: https://help.dragen.illumina.com/reference/dragen-application-manager

This command retrieves detailed usage information for a specific installed application, including its provider, name, and version. It outlines the required parameters, flags, and resources needed to run the application.

```shell
> dragen-app-manager help
How to get application help. 

[Application]
- Provider: Illumina
- Name: SimpleApp
- Version: 1.0.0
Usage:
dragen-app-manager help --provider Illumina --name SimpleApp --version 1.0.0
```

```shell
> dragen-app-manager help --provider Illumina --name SimpleApp --version 1.0.0

SimpleApp version 1.0.0 provided by Illumina

This requires the parameter "A" to be set with the value "B",
a Flag must be explicitly set to either true or false,
and a Count with a value greater than 0.
There is also an example of representing a number as a string. 

[Environment] 

--environment TZ=<value>
Description: Timezone

[Settings] 

--setting simple=<value>
Description: A simple setting that is a filename

[Parameters] 

--param.A
Description: A required parameter with an required value of B. 

--param.Flag
Description: A flag must be explicitly set. 

--param.Count
Description: A number. 

--param.NumberString
Description: A number as a string

[Resources] 

--resource opt=<value>
Description: the /opt directory

Usage:
dragen-app-manager dry-run --provider Illumina --name SimpleApp --version 1.0.0 --inputDirectory input --outputDirectory output --environment TZ=EST --setting simple=config.json --resource opt=/opt --param.A B --param.Flag true --param.Count 1 --param.NumberString '"1532554234"'
```

--------------------------------

### Make Installer Executable

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation

Ensures the DRAGEN pipeline installer has the necessary execute permissions before launching. This is a crucial step for successful installation.

```shell
chmod +x install_Solid_WGS_TN_v{version}.run
```

--------------------------------

### Install Application or Resource (Shell)

Source: https://help.dragen.illumina.com/reference/dragen-application-manager

This command installs applications or resources into the Dragen environment. It requires a '--file' argument specifying the path to the application (.iapp) or resource (.ires) file. Resource dependencies must be installed prior to application installation.

```shell
dragen-app-manager install --file ./application.iapp
dragen-app-manager install --file ./resource.ires
```

--------------------------------

### Dragen Explify Pipeline Command Line Example

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/pipeline

This example demonstrates how to run the Dragen Explify Analysis Pipeline using various command-line options. It includes essential parameters like enabling the pipeline, specifying output locations, providing input sample lists, defining the test panel, and setting resource allocation.

```bash
dragen \
  --enable-explify=true \
  --output-file-prefix <PREFIX> \
  --explify-sample-list /path/to/sample/list/tsv \
  --explify-test-panel-name <"RPIP"/"UPIP"/"VSPv2"/"Custom"> \
  --explify-test-panel-version <VERSION> \
  --explify-ref-db-dir /path/to/root/db/dir \
  --explify-load-db-ram=true \
  --output-directory <OUTPUT_DIR> \
  --intermediate-results-dir <OUTPUT_DIR> \
  --explify-ncpus=1
```

--------------------------------

### DRAGEN Plasma Contamination Detection Command Line Example

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/mrd

Example command-line invocation for running the DRAGEN plasma contamination detection module. This setup requires specifying input FASTQ files, reference directories, and output locations.

```bash
/opt/dragen/$VERSION/bin/dragen           # DRAGEN install path 
--ref-dir $REF_DIR                        # path to DRAGEN linear hashtable
--validate-pangenome-reference=false      # required
--output-directory $OUTPUT 
--intermediate-results-dir $PATH     
--output-file-prefix $PREFIX 
# Inputs (e.g. FQ list) 
--fastq-list $PATH                    
--fastq-list-sample-id $STRING

```

--------------------------------

### Heme Pipeline Self-Test Success Output

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation

Example output indicating a successful Heme pipeline installation and configuration. This confirms that the pipeline is ready for use.

```text
Checking system configuration...OK!
Now running a test execution of the pipeline.
This could take up to 15 minutes...
Verifying analysis output.
Successfully validated test analysis results.
SUCCESS!
DRAGEN Heme WGS Tumor Only Pipeline is correctly configured and ready for use.
```

--------------------------------

### Configure Explify Analysis Pipeline with Databases

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/pipeline

This configuration sets up the Explify Analysis Pipeline to use specific database files. It requires the directory where databases are stored, the test panel name, and its version. Loading databases into RAM can improve performance.

```bash
# Example configuration for RPIP 6.7.0
--explify-ref-db-dir /explify-databases
--explify-test-panel-name RPIP
--explify-test-panel-version 6.7.0

# Recommended for databases on normal file systems
--explify-load-db-ram=true

# Recommended for databases on RAM disks
--explify-load-db-ram=false
```

--------------------------------

### Example Splice Variant Fusion Genes File

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-rna-pipeline/splice-variant-caller

This example demonstrates the format for specifying known splice variant fusions. Lines starting with '#' are ignored. Single gene names indicate intra-genic fusions, while two gene names on a line indicate inter-genic fusions.

```plaintext
# Force the below splice variant genes (intra and inter genic) to fusion caller 
EGFR
AJM1 PHPT1
```

--------------------------------

### Install DRAGEN Licenses Automatically (Connected)

Source: https://help.dragen.illumina.com/reference/licensing/onprem_licensing

This command forces the DRAGEN server to automatically download and install all available licenses assigned to it from the Illumina License Server. It requires root privileges. For specific licenses like PipSeq or GvcfGenotyper on older DRAGEN versions, explicit calls with the -f option might be necessary.

```bash
sudo dragen_lic -i auto
```

```bash
sudo dragen_lic -i auto -f PipSeq
```

```bash
sudo dragen_lic -i auto -f GvcfGenotyper
```

--------------------------------

### Run DRAGEN Targeted Caller from FASTQ Input

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller

This command-line example demonstrates how to run the DRAGEN Targeted Caller using FASTQ files as input. It specifies the reference genome, input FASTQ files, output directory, and enables the targeted caller.

```bash
dragen \
	-r /staging/human/reference/hg38_alt_aware/DRAGEN/${HASH_TABLE_VERSION} \
	--fastq-file1 /staging/test/data/NA12878_R1.fastq \
	--fastq-file2 /staging/test/data/NA12878_R2.fastq \
	--output-directory /staging/test/output \
	--output-file-prefix NA12878_dragen \
	--RGID DRAGEN_RGID \
	--RGSM NA12878 \
	--enable-targeted=true
```

--------------------------------

### Start Dragen Analysis on ICA Cloud using icav2 client

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/quick-start

This command initiates a Dragen analysis on the ICA cloud platform using the 'icav2' client. It requires specifying project ID, storage size, input files, and various analysis parameters like reference genome and sample IDs.

```sh
icav2 projectpipelines start nextflow ${PIPELINE_ID} \
--project-id ${ANY_PROJECT_ID} \
--storage-size Large \
-o json \
--input ${ANY_SAMPLE_SHEET} \
--input ${ANY_INPUT_DIR} \
--parameters inputType:'bcl' \
--parameters referenceGenome:'hg38' \
--parameters oraCompressionEnabled:'true' \
--parameters sampleIds:'1267-Prostate-Del-R1,741-Lung-SNV-R1' \
--user-reference ${ANY_USER_REFERENCE}
```

--------------------------------

### Example Knowns List for Splice Variants

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-rna-pipeline/splice-variant-caller

This example demonstrates the format of a 'knowns' list file, used as a whitelist for splice variants. It's a tab-separated file where the first four columns specify the splice junction coordinates (contig, start, end, strand). Additional columns are present but not evaluated for filtering.

```text
chr7	116771655	116774880	1	0	0	0	0	0
chr7	55019366	55155829	1	0	0	0	0	0
chrX	67686127	67694672	1	0	0	0	0	0
```

--------------------------------

### List Downloaded Explify Reference Databases

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/pipeline

This command lists the Explify reference databases that have already been downloaded to the specified directory. The `-d` argument indicates the storage directory, and an optional `-p` argument can filter the list by a specific test panel name.

```shell
./explify-dbs.sh list -d explify-databases/
```

--------------------------------

### Get General Help (Shell)

Source: https://help.dragen.illumina.com/reference/dragen-application-manager

This command displays general help information for the Dragen Application Manager. It's the starting point for understanding the available commands and their basic usage.

```shell
dragen-app-manager help
```

--------------------------------

### Run DRAGEN with FASTQ UMI Input

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-dna-pipeline/unique-molecular-identifiers

This example demonstrates running DRAGEN with UMIs sourced directly from FASTQ files. It uses the '--umi-source=fastq' and '--umi-fastq' options to specify the UMI FASTQ file. The UMI library type can be adjusted to 'random-simplex' or 'random-duplex'.

```bash
dragen \
-r <REF> \
-1 <FQ1> \
-2 <FQ3> \
--umi-source=fastq \
--umi-fastq <FQ2> \
--output-dir <OUTPUT> \
--output-file-prefix <PREFIX> \
--enable-map-align true \
--enable-sort true \
--umi-library-type nonrandom-duplex \
--umi-metrics-interval-file [valid target BED file]
```

--------------------------------

### Download a Specific Explify Reference Database

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/pipeline

This command downloads a specified Explify reference database using the `explify-dbs.sh` script. It requires the database directory (`-d`), test panel name (`-p`), and version (`-v`). The `-n` argument allows specifying the number of CPUs for faster downloading.

```shell
./explify-dbs.sh download -d explify-databases/ -p UPIP -v 8.8.0 -n 20
```

--------------------------------

### DRAGEN License Server Healthcheck Response

Source: https://help.dragen.illumina.com/reference/licensing/onprem_licensing

This is an example of a successful response from the DRAGEN License Server's healthcheck endpoint. A 200 status code and a JSON body containing the server version indicate that the server is reachable and operational.

```json
{"version":"<server version>"}
```

--------------------------------

### Run DRAGEN 16S Analysis with Paired-End Reads and Pre-built Database

Source: https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-16s-pipeline

This example demonstrates how to run the DRAGEN 16S pipeline using paired-end FASTQ files and a pre-built reference database. It specifies essential inputs like output prefixes and directories, FASTQ files, and the database location, along with the number of threads for processing.

```bash
/opt/dragen/$VERSION/bin/dragen
--enable-16s true
--output-file-prefix analysis1
--output-directory /path/to/output/
--16s-fastq1 /path/to/input/sampleA_S1_L001_R1_001.fastq.gz
--16s-fastq2 /path/to/input/sampleA_S1_L001_R2_001.fastq.gz
--16s-db-dir /path/to/databases/Refseq-RDP-v1/1.0.1/
--num-threads 20
```

--------------------------------

### List Applications and Resources

Source: https://help.dragen.illumina.com/reference/dragen-application-manager

Provides a list of all installed applications and available resources. The '--detailed' flag offers more comprehensive information. Output can be parsed with 'jq'.

```shell
dragen-app-manager list

dragen-app-manager list | jq

dragen-app-manager list --detailed | jq
```

--------------------------------

### Execute DRAGEN Batch Task

Source: https://help.dragen.illumina.com/reference/dragen-multi-cloud/azure-batch/run-azure-modes

Bash command to execute a DRAGEN task within an Azure Batch job. It handles file extraction, DRAGEN execution with specified parameters, and output directory setup. Assumes DRAGEN is installed and tarball is available.

```bash
/bin/bash -c \
"mkdir <Hash table reference directory> <Output directory>; \
tar xzvf dragen.tar -C <Hash table reference directory>; \
/opt/edico/bin/dragen --partial-reconfig HMM --ignore-version-check true; \
/opt/edico/bin/dragen -f -r <Hash table reference directory> \
-1 <Path to the first local FASTQ file on the node> \
-2 <Path to the second local FASTQ file on the node> \
--RGID <RGID associated with the DRAGEN run> \
--RGSM <RGSM associated with the DRAGEN run> \
--enable-bam-indexing true \
--enable-map-align-output true \
--enable-sort true \
--output-file-prefix dragen-batch \
--enable-map-align true \
--output-format BAM \
--output-directory <Output directory> \
--enable-variant-caller true \
--lic-server <DRAGEN license>"
```
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