DRAGEN Reference Support

DRAGEN supports the construction of reference hash tables for both human and non-human reference genomes. The reference autodetect feature of DRAGEN is able to recognize the reference hash tables build on the four Human reference genomes: hg19 (hg19), GRCh37/hs37d5 (hs37d5), GRCh38/hs38d1(hg38), and T2T-CHM13v2.0 (chm13).

DRAGEN supports pangenome reference hash tables which extend the reference genomes with alternative variant paths from a sample cohort used to construct the pangenome reference. A pangenome-based reference improves the mapping accuracy of Illumina reads in the “Difficult-to-Map Regions” of the genome and the downstream variant calling.

Pre-built human references are available for download at DRAGEN Software Support Site page.

The pangenome is the recommended for Germline human analyses. The accuracy achieved with pangenome references are highlighted in the plot below.

In the following tables we summarize the reference support for each DRAGEN component and the recommended reference type for each component.

Germline

Component
Recommended Human Reference Type
Recommended Non-Human Reference Type
Human hg19
Human hs37d5
Human hg38
Human chm13
Non-Human

SNV

Pangenome

Linear

Yes

Yes

Yes

Yes

Yes

CNV

Pangenome

Linear

Yes

Yes

Yes

Yes*

No

SV

Pangenome

Linear

Yes

Yes

Yes

Yes*

Yes

Expansion Hunter

Pangenome

Linear

Yes

Yes

Yes

No

No

Targeted Callers

Pangenome

Linear

Yes

Yes

Yes

No

No

RNA

Linear

Linear

Yes

Yes

Yes

Yes*

Yes

De Novo

Pangenome

Linear

Yes

Yes

Yes

Yes*

Yes

Joint Genotyping

Pangenome

Linear

Yes

Yes

Yes

Yes*

Yes

Biomarkers (HLA)

Pangenome

Linear

Yes

Yes

Yes

Yes*

No

gVCF genotyper

Pangenome

Linear

Yes

Yes

Yes

Yes*

Yes

Somatic

Component
Recommended Human Reference Type
Recommended Non-Human Reference Type
Human hg19
Human hs37d5
Human hg38
Human chm13
Non-Human

SNV

Linear

Linear

Yes

Yes

Yes

Yes*

No

UMI SNV

Linear

Linear

Yes

Yes

Yes

Yes*

No

CNV

Linear

Linear

Yes

Yes

Yes

Yes*

No

SV

Linear

Linear

Yes

Yes

Yes

Yes*

No

Methylation

Component
Recommended Human Reference Type
Recommended Non-Human Reference Type
Human hg19
Human hs37d5
Human hg38
Human chm13
Non-Human

Methylation

Linear

Linear

Yes

Yes

Yes

No

No

Annotation

Component
Recommended Human Reference Type
Recommended Non-Human Reference Type
Human hg19
Human hs37d5
Human hg38
Human chm13
Non-Human

Nirvana

Pangenome

Linear

Yes

Yes

Yes

No

Yes

* DRAGEN supports the component execution, however the component's accuracy has not been established.

See Prepare a Reference Genome for how to build a custom reference genome.

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