DRAGEN Pipelines and Apps | Tools for genomic data analysis

DRAGEN apps and pipelines

A powerful and scalable analysis environment for interpreting and visualizing multiomic data

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Application	DRAGEN On-Premises Server	NovaSeq X Series	NextSeq 1000/2000	MiSeq i100 Series	BaseSpace Sequence Hub	Illumina Connected Analytics
BCL Convert	checkmark	checkmark	checkmark	checkmark	checkmark	custom only
DRAGEN ORA Compression	checkmark	checkmark	checkmark	checkmark		checkmark
Whole genome	Germline + somatic	Germline + somatic	Germline only		Germline + somatic	Germline + somatic
Enrichment (including exome)	Germline + somatic	Germline + somatic	Germline + somatic		Germline + somatic	Germline + somatic
RNA	checkmark	checkmark	checkmark		checkmark	checkmark
TruSight Oncology 500 Portfolio	checkmark				checkmark	checkmark
Amplicon	checkmark		DNA only		checkmark	checkmark
Single-Cell RNA	checkmark		checkmark		checkmark	checkmark
NanoString GeoMx NGS (spatial transcriptomics)			checkmark		checkmark
Methylation	checkmark	checkmark			checkmark	checkmark
Protein quantification	checkmark				checkmark	checkmark
Imputation	checkmark				checkmark	checkmark
PGx Star Allele Caller	checkmark				checkmark	checkmark
Illumina Complete Long Reads					checkmark	checkmark
VSP, RVEK, RPIP, UPIP	checkmark			checkmark	checkmark	Beta
COVID, IMAP, IMAP-FLU					checkmark
Metagenomics*	checkmark				checkmark
Small WGS				checkmark	checkmark
Heme WGS^†	checkmark					checkmark
Solid tumor normal WGS	checkmark					checkmark

Application

DRAGEN On-Premises Server

NovaSeq X Series

NextSeq 1000/2000

MiSeq i100 Series

BaseSpace Sequence Hub

Illumina Connected Analytics

BCL Convert

checkmark

custom only

DRAGEN ORA Compression

checkmark

Whole genome

Germline + somatic

Germline only

Germline + somatic

Enrichment (including exome)

Germline + somatic

RNA

checkmark

TruSight Oncology 500 Portfolio

checkmark

Amplicon

checkmark

DNA only

checkmark

Single-Cell RNA

checkmark

NanoString GeoMx NGS (spatial transcriptomics)

checkmark

Methylation

checkmark

Protein quantification

checkmark

Imputation

checkmark

PGx Star Allele Caller

checkmark

Illumina Complete Long Reads

checkmark

VSP, RVEK, RPIP, UPIP

checkmark

Beta

COVID, IMAP, IMAP-FLU

checkmark

Metagenomics*

checkmark

Small WGS

checkmark

Heme WGS^†

checkmark

Solid tumor normal WGS

checkmark

Pipeline	Description	Variant types detected^a	Metrics provided	Publications
DRAGEN Demultiplexing	Performs rapid demultiplexing of NGS analysis
DRAGEN ORA Compression	Optimized for high compression ratios of FASTQ files, as well as rapid compression and decompression, while preserving data integrity		Compression ratio Run time	Design considerations and methodology
DRAGEN Map + Align	Can be run as a standalone or as part of DRAGEN’s suite of pipelines		Mapping metrics Duration metrics Coverage metrics	Identification of SARS-CoV-2 variants Accurate and efficient calling of small and large variants
DRAGEN Germline	Provides NGS analysis, including targeted callers for carrier screening, PGx, and more, mosaic variant calling, de-novo variant discovery with Multi-Region Joint Detection (MRJD), and repeat expansion detection and genotyping through Illumina Expansion Hunter.	SNV Indel CNV SV Repeat expansions	Mapping metrics Duration metrics Coverage metrics Variant metrics Callability report	Rapid whole-genome sequencing Metabolomics research Rare variant contribution to human disease
DRAGEN Somatic	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 Indel CNV SV TMB MSI HLA	Mapping metrics Duration metrics Coverage metrics Variant metrics Callability report	Mutational landscape in multiple myeloma Clonal evolution in multiple myeloma Cancer variant calling
DRAGEN Enrichment	Combines DRAGEN germline and somatic callers into a pipeline designed specifically for analyzing enrichment samples. Includes a full suite of enrichment metrics and reporting	SNV Indel CNV SV	Mapping metrics Duration metrics Coverage metrics Variant metrics Callability report	Pediatric FLNC variants Clonal dynamics in composite lymphoma
DRAGEN RNA	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).	SNV Indel Gene fusion	Mapping metrics Duration metrics Coverage metrics Variant metrics Callability report
DRAGEN Single Cell RNA	Performs demultiplexing, cell-barcode and UMI error correction, sequence alignment, and quantification of gene expression		Mapping metrics Duration metrics Coverage metrics Callability report Cell metrics
DRAGEN Joint Genotyping	Calls variants jointly across multiple genomes and scales to large cohorts of samples at expedited speeds with uncompromising accuracy	SNV Indel CNV SV Repeat expansions	Mapping metrics Duration metrics Coverage metrics Variant metrics Callability report	A hybrid cloud system for large-scale human genomic research
DRAGEN Methylation	Performs alignment and methyl calling. Calculates alignment and methylation metrics.		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
DRAGEN TruSight Oncology 500 ctDNA Analysis Software	Offers secondary analysis support for TruSight Oncology 500 ctDNA. Only available on the local DRAGEN Server (version 3)	SNV Indel CNV DNA fusions MSI TMB	Mapping metrics Duration metrics Coverage metrics Variant metrics Callability report	Development of blood TMB reference materials for validating cfDNA assays
DRAGEN Imputation	Enables scalable low-pass whole-genome sequencing analysis in a user-friendly tool	SNV Indel		Boosting variant calling performance

Pipeline

Description

Variant types detected^a

Metrics provided

Publications

DRAGEN Demultiplexing

Performs rapid demultiplexing of NGS analysis

DRAGEN ORA Compression

Optimized for high compression ratios of FASTQ files, as well as rapid compression and decompression, while preserving data integrity

Compression ratio
Run time

Design considerations and methodology

DRAGEN Map + Align

Can be run as a standalone or as part of DRAGEN’s suite of pipelines

Mapping metrics
Duration metrics
Coverage metrics

Identification of SARS-CoV-2 variants

Accurate and efficient calling of small and large variants

DRAGEN Germline

Provides NGS analysis, including targeted callers for carrier screening, PGx, and more, mosaic variant calling, de-novo variant discovery with Multi-Region Joint Detection (MRJD), and repeat expansion detection and genotyping through Illumina Expansion Hunter.

SNV
Indel
CNV
SV
Repeat expansions

Mapping metrics
Duration metrics
Coverage metrics
Variant metrics
Callability report

Rapid whole-genome sequencing

Metabolomics research

Rare variant contribution to human disease

DRAGEN Somatic

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
Indel
CNV
SV
TMB
MSI
HLA

Mapping metrics
Duration metrics
Coverage metrics
Variant metrics
Callability report

Mutational landscape in multiple myeloma

Clonal evolution in multiple myeloma

Cancer variant calling

DRAGEN Enrichment

Combines DRAGEN germline and somatic callers into a pipeline designed specifically for analyzing enrichment samples. Includes a full suite of enrichment metrics and reporting

SNV
Indel
CNV
SV

Mapping metrics
Duration metrics
Coverage metrics
Variant metrics
Callability report

Pediatric FLNC variants

Clonal dynamics in composite lymphoma

DRAGEN RNA

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).

SNV
Indel
Gene fusion

Mapping metrics
Duration metrics
Coverage metrics
Variant metrics
Callability report

DRAGEN Single Cell RNA

Performs demultiplexing, cell-barcode and UMI error correction, sequence alignment, and quantification of gene expression

Mapping metrics
Duration metrics
Coverage metrics
Callability report
Cell metrics

DRAGEN Joint Genotyping

Calls variants jointly across multiple genomes and scales to large cohorts of samples at expedited speeds with uncompromising accuracy

SNV
Indel
CNV
SV
Repeat expansions

Mapping metrics
Duration metrics
Coverage metrics
Variant metrics
Callability report

A hybrid cloud system for large-scale human genomic research

DRAGEN Methylation

Performs alignment and methyl calling. Calculates alignment and methylation metrics.

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

DRAGEN TruSight Oncology 500 ctDNA Analysis Software

Offers secondary analysis support for TruSight Oncology 500 ctDNA. Only available on the local DRAGEN Server (version 3)

SNV
Indel
CNV
DNA fusions
MSI
TMB

Mapping metrics
Duration metrics
Coverage metrics
Variant metrics
Callability report

Development of blood TMB reference materials for validating cfDNA assays

DRAGEN Imputation

Enables scalable low-pass whole-genome sequencing analysis in a user-friendly tool

SNV
Indel

Boosting variant calling performance

DRAGEN apps and pipelines

Access more applications on a single platform

Key DRAGEN apps and availability