DRAGEN Applications

Applications

DRAGEN analysis offers a large selection of application pipelines.

Pipeline	Description	Variant Types Detected	Metrics Provided
DRAGEN Demultiplexing	Rapid demultiplexing of NGS analysis	N/A	N/A
DRAGEN Compression	DRAGEN ORA compression is optimized for high compression ratios of FASTQ files, as well as rapid compression and decompression, all while preserving data integrity.	N/A	Compression Ratio Run Time
DRAGEN Map + Align	The DRAGEN Map + Align can be run as a standalone or as part of DRAGEN’s suite of pipelines	N/A	Mapping metrics Duration Metrics Coverage Metrics
DRAGEN Germline	The DRAGEN Germline Pipeline provides end-to-end NGS analysis, including advanced error model calibration for increased accuracy, and repeat expansion detection and genotyping through Illumina Expansion Hunter.	SNV CNV SV Repeat Expansions	Mapping metrics Duration Metrics Coverage Metrics Variant Metrics Callability Report
DRAGEN Somatic	The DRAGEN Somatic Pipeline includes tumor-only and tumor–normal modes, designed for detecting somatic variants in tumor samples. Both modes make no ploidy assumptions, enabling detection of low-frequency alleles.	SNV CNV SV TMB MSI HLA	Mapping metrics Duration Metrics Coverage Metrics Variant Metrics Callability Report
DRAGEN Enrichment	The DRAGEN Enrichment Pipeline combines DRAGEN’s germline and somatic callers into a pipeline designed specifically for analyzing enrichment samples. Includes a full suite of enrichment metrics and reporting.	SNV CNV SV	Mapping metrics Duration Metrics Coverage Metrics Variant Metrics Callability Report
DRAGEN RNA	The DRAGEN RNA Pipeline performs transcriptome analysis starting with splice junction discovery and alignment, followed by rapid alignment and splice junction mapping and quantification. For differential expression, Illumina recommends the DRAGEN Differential Expression app on BaseSpace Sequence Hub.	Gene fusion	Mapping metrics Duration Metrics Coverage Metrics Variant Metrics Callability Report
DRAGEN Single Cell RNA	The DRAGEN Single Cell RNA pipeline performs demultiplexing, cell-barcode and UMI error correction, sequence alignment, and quantification of gene expression.	N/A	Mapping Metrics Duration Metrics Coverage Metrics Callability Report Cell Metrics
DRAGEN Joint Genotyping	The DRAGEN Joint Genotyping/Population Pipeline calls variants jointly across multiple genomes and scales to large cohorts of samples at expedited speeds with uncompromising accuracy.	SNV CNV SV Repeat Expansions	Mapping metrics Duration Metrics Coverage Metrics Variant Metrics Callability Report
DRAGEN Methylation	The DRAGEN Methylation Pipeline performs alignment, methyl calling, and calculates alignment and methylation metrics.	N/A	Mapping metrics Duration Metrics Coverage Metrics Variant Metrics Callability Report
DRAGEN Reference Builder	Accepts FASTA files, and builds the proprietary reference used by the DRAGEN apps.	N/A	N/A
DRAGEN TruSight Oncology 500 ctDNA Analysis Software	Secondary analysis support for Illumina’s TruSight Oncology 500 ctDNA. Available on the local DRAGEN Server version 3 and later.	SNV CNV DNA fusions MSI TMB	Mapping metrics Duration Metrics Coverage Metrics Variant Metrics Callability Report
DRAGEN Imputation	The DRAGEN Imputation pipeline is an end to end user friendly tool that enables scalable low pass whole genome sequencing analysis	N/A	Impute ≤100 samples simultaneously 1.7x faster compared to original GLIMPSE code

Available Platforms

DRAGEN analysis is available on multiple platforms.

Platform	Description
DRAGEN on-premises server	DRAGEN on-premises server offers highly accurate secondary analysis in a fraction of time compared with a traditional CPU-based system. - Analyze and store data locally - Supports varying levels of command line interface - Replace up to 30 traditional compute instances - Fully process a 34× whole human genome in ~30 minutes. (1) - One unit supports two NovaSeq 6000 Systems running at full capacity
DRAGEN analysis on Illumina Connected Analytics	Couples the accuracy and speed of the DRAGEN with the ability to customize analysis pipeline to operationalize informatics on a secure platform.
DRAGEN on BaseSpace Sequence Hub (BSSH)	Push button analysis capability in an intuitive, easy-to-use interface with compliance, and storage features of BaseSpace Sequence Hub and Amazon Web Services (AWS).
DRAGEN onboard NovaSeq X Series	- Flexibly runs multiple secondary analysis pipelines in parallel. - Performs up to four simultaneous applications per flow cell in a single run. - Brings up to 5x lossless data compression, and analysis with supported applications - Provides savings on analysis, which over five years can exceed the price of the sequencer
DRAGEN onboard NextSeq 1000 and NextSeq 2000 Systems	- Provides access to select DRAGEN analysis informatics pipelines - Enables users to generate results in as little as two hours - Uses intuitive pipeline algorithms to reduce reliance on external informatics experts
DRAGEN on AWS, Azure	DRAGEN supports the FPGA enabled instance types of AWS, Azure. Rpm installers and the Kernel driver can be installed on images managed by the user, and DRAGEN can be run by purchasing a license.
DRAGEN on AWS and Azure Marketplace	Pre-configured Amazon Machine Images (AMI) and Azure Virtual Machines with DRAGEN installed can be accessed from the respective marketplace offerings in a Pay-As-You-Use model.
DRAGEN on GCP	DRAGEN is made available on the Google Cloud Platform. Pre-configured instances with DRAGEN installed can be accessed through the GCP application interface. Limited availability. Please reach out to your Illumina representative for access.

(1) HG002 from PrecisionFDA truth challenge V2 run with DRAGEN analysis v4.0 on DRAGEN server v4, all callers

Analysis Uses

DRAGEN analysis can be used in numerous fields in the biological sciences.

Analysis	Description
Genetic Diseases	Reduce time required for genomic analysis, with high accuracy and comprehensiveness
Oncology	Analyze tumor-only and tumor/normal samples with accuracy, comprehensiveness, and efficiency
Cell and Molecular Biology	Advance understanding of cellular mechanisms with rapid analysis pipelines for bulk and single cell samples
Population Genomics	Accurately and efficiently analyze sequenced genomes at scale. Accelerate re-analysis as computational tools improve over time
Infectious Disease	Detect and characterize infectious diseases with a comprehensive solution
Agrigenomics	Efficiently analyze animals and plants of varying genomic complexities with custom reference