DRAGEN secondary analysis apps and pipelines

Support a wide range of NGS methods, including WGS, RNA-seq, exome/enrichment, amplicon, 16S metagenomics, and more  

Access more applications on a single platform

DRAGEN secondary analysis provides applications and pipelines for a wide range of genomic analysis capabilities. DRAGEN apps offer accurate, efficient, and secure analysis in the cloud on BaseSpace Sequence Hub. DRAGEN pipelines are data analysis tools that can be launched via an on-premises server, in the cloud on Illumina Connected Analytics, or onboard the NextSeq 1000 and NextSeq 2000 Systems and NovaSeq X Series.

Key DRAGEN apps and availability

Application DRAGEN On-Premises Server NovaSeq X Series NextSeq 1000/2000 BaseSpace Sequence Hub Illumina Connected Analytics
BCL Convert
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DRAGEN ORA Compression
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custom only
DRAGEN FASTQ + MultiQC
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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
DRAGEN Amplicon
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  DNA only
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RNA
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Single-Cell RNA
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NanoString GeoMx NGS (spatial transcriptomics)    
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Methylation
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Metagenomics
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COVID COVIDSeq, COVID lineage   COVIDSeq (cloud only) COVIDSeq, COVID lineage  
TruSight Oncology 500 Portfolio
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ScATAC-Seq (single-cell sequencing assay for transposase-accessible chromatin)
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Imputation
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PGx Star Allele Caller
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Illumina Complete Long Reads      
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RPIP and UPIP panels
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Beta

*Metagenomics applications enabled by Kmer classifier. More tools coming soon.

TruSight Oncology 500 Portfolio for BaseSpace Sequence Hub: Illumina Connected Analytics subscription required

DRAGEN pipelines

Pipeline Description Variant types detecteda 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 the  
  • 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 advanced error model calibration for increased accuracy 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
Identifying point mutations in Bangladeshi SARS-CoV-2 strains
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

a. SNV, single nucleotide variant; CNV, copy number variation; SV, small variant; TMB, tumor mutational burden; MSI, microsatellite instability; HLA, human leukocyte antigen

Featured DRAGEN applications

Learn more or get in touch

View more details about DRAGEN analysis features, learn how to order, and find product documentation. You can also speak to a specialist to get your questions answered.