DRAGEN Reference Support
DRAGEN supports the construction of a 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). Pre-built human reference hash tables are available for download at Illumina DRAGEN Bio-IT Platform Support Site page.
DRAGEN also supports multigenome reference graphs hash tables which extend the reference genomes with alternative variant paths from a sample cohort used to construct the multigenome reference. A graph-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 multigenome reference graphs are available for download at Illumina DRAGEN Bio-IT Platform Support Site page.
Refer to the following information, which summarize the reference support for each DRAGEN component and the recommended reference type for each component.
Germline
|
|
Human hg19 |
Human hs37d5 |
Human hg38 |
Human chm13 |
Non-Human |
Recommended Human Reference Type |
Recommended Non-Human Reference Type |
|---|---|---|---|---|---|---|---|
|
SNV |
Yes |
Yes |
Yes |
Yes |
Yes |
Graph |
Non-Graph |
|
CNV |
Yes |
Yes |
Yes |
Yes¹ |
No |
Graph |
Non-Graph |
|
SV |
Yes |
Yes |
Yes |
Yes¹ |
Yes |
Graph |
Non-Graph |
|
Expansion Hunter |
Yes |
Yes |
Yes |
No |
No |
Graph |
Non-Graph |
|
Targeted Callers |
Yes |
Yes |
Yes |
No |
No |
Graph |
Non-Graph |
|
RNA |
Yes |
Yes |
Yes |
Yes¹ |
Yes |
Non-Graph |
Non-Graph |
|
De Novo |
Yes |
Yes |
Yes |
Yes¹ |
Yes |
Graph |
Non-Graph |
|
Joint Genotyping |
Yes |
Yes |
Yes |
Yes¹ |
Yes |
Graph |
Non-Graph |
|
Biomarkers (HLA) |
Yes |
Yes |
Yes |
Yes¹ |
No |
Graph |
Non-Graph |
|
gVCF genotyper |
Yes |
Yes |
Yes |
Yes¹ |
Yes |
Graph |
Non-Graph |
1. The accuracy has not been established.
Somatic
|
|
Human hg19 |
Human hs37d5 |
Human hg38 |
Human chm13 |
Non-Human |
Recommended Human Reference Type |
Recommended Non-Human Reference Type |
|---|---|---|---|---|---|---|---|
|
SNV |
Yes |
Yes |
Yes |
Yes¹ |
No |
Non-Graph |
Non-Graph |
|
UMI SNV |
Yes |
Yes |
Yes |
Yes¹ |
No |
Non-Graph |
Non-Graph |
|
CNV |
Yes |
Yes |
Yes |
Yes¹ |
No |
Non-Graph |
Non-Graph |
|
SV |
Yes |
Yes |
Yes |
Yes¹ |
No |
Non-Graph |
Non-Graph |
1. The accuracy has not been established.
Methylation
|
|
Human hg19 |
Human hs37d5 |
Human hg38 |
Human chm13 |
Non-Human |
Recommended Human Reference Type |
Recommended Non-Human Reference Type |
|---|---|---|---|---|---|---|---|
|
Methylation |
Yes |
Yes |
Yes |
No |
No |
Non-Graph |
Non-Graph |
Annotation
|
|
Human hg19 |
Human hs37d5 |
Human hg38 |
Human chm13 |
Non-Human |
|---|---|---|---|---|---|
|
Nirvana |
Yes |
Yes |
Yes |
No |
Yes |
