Illumina DRAGEN Bio-IT Platform Product Files

Reference Files

Assembly Type Reference Genome Hash Table File Name Major DRAGEN Version   3.8 3.9 3.10 4.0 4.2 4.3
Hash Table Version   8 8 8 8 9 10
CHM13 Multigenome (Graph) reference Homo sapiens [T2T] CHM13_v2 v4 Multigenome chm13_v2-cnv.graph.hla.rna-10-r4.0-1
10            
Homo sapiens [T2T] CHM13_v2 v3 Multigenome chm13_v2-cnv.graph.hla.rna-9-r3.0-1 9          
Linear reference Homo sapiens [T2T] CHM13_v2 v4 chm13_v2-cnv.hla.methylated_combined.rna-10-r4.0-1 10            
Homo sapiens [T2T] CHM13_v2 v3 chm13_v2-cnv.hla.rna-9-r3.0-1 9          
hg19 Multigenome (Graph) reference Homo sapiens [UCSC] hg19 v4 Multigenome hg19-alt_masked.cnv.graph.hla.rna-10-r4.0-1 10            
Homo sapiens [UCSC] hg19 v3 Multigenome hg19-alt_masked.cnv.graph.hla.rna-9-r3.0-1 9          
Homo sapiens [UCSC] hg19 v2 Multigenome hg19-alt_masked.cnv.graph.hla.rna-8-r2.0-1.run 8            
Homo sapiens [UCSC] hg19 v2 Multigenome hg19_alt_masked_graph_v2+cnv+graph+rna-8-1644018758-1 8            
Homo sapiens [UCSC] hg19 alt-masked Multigenome hg19_alt_masked+cnv+graph+rna-8-r1.0-1 8            
Homo sapiens [UCSC] hg19 alt-aware Multigenome hg19_alt_aware+cnv+graph+rna-8-r1.0-0
8        
Linear reference Homo Sapiens [UCSC] hg19 v4 hg19-alt_masked.cnv.hla.methylated_combined.rna-10-r4.0-1.tar
10            
Homo Sapiens [UCSC] hg19 v3 hg19-alt_masked.cnv.hla.rna-9-r3.0-1 9            
Homo sapiens [UCSC] hg19 methylation v3 hg19-alt_masked.methylated_combined.methylation.seed_len27-9-r3.0-1 9            
Homo sapiens [UCSC] hg19 v2 hg19-alt_masked.cnv.hla.rna-8-r2.0-1 8            
hg38 Multigenome (Graph) reference Homo sapiens [1000 Genomes] hg38 v4 Multigenome hg38-alt_masked.cnv.graph.hla.rna-10-r4.0-1 10            
Homo sapiens [1000 Genomes] hg38 v3 Multigenome hg38-alt_masked.cnv.graph.hla.rna-9-r3.0-1 9          
Homo sapiens [1000 Genomes] hg38 v2 Multigenome hg38-alt_masked.cnv.graph.hla.rna-8-r2.0-1 8            
Homo sapiens [1000 Genomes] hg38 v2 Multigenome hg38_alt_masked_graph_v2+cnv+graph+rna-8-1644018559-1 8            
Homo sapiens [1000 Genomes] hg38 alt-masked Multigenome hg38_alt_masked+cnv+graph+rna-8-r1.0-1 8            
Homo sapiens [1000 Genomes] hg38 alt-aware Multigenome hg38_alt_aware+cnv+graph+rna-8-r1.0-0 8        
Linear reference Homo sapiens [1000 Genomes] hg38 v4 hg38-alt_masked.cnv.hla.methylated_combined.rna-10-r4.0-1 10            
Homo sapiens [1000 Genomes] hg38 v3
hg38-alt_masked.cnv.hla.rna-9-r3.0-1 9            
Homo sapiens [1000 Genomes] hg38 methylation v3
hg38-alt_masked.methylated_combined.methylation.seed_len27-9-r3.0-1 9            
Homo sapiens [1000 Genomes] hg38 v2 hg38-alt_masked.cnv.hla.rna-8-r2.0-1 8            
hs37d5 Multigenome (Graph) reference Homo sapiens [NCBI] hs37d5 v4 Multigenome hs37d5-cnv.graph.hla.rna-10-r4.0-1 10            
Homo sapiens [NCBI] hs37d5 v3 Multigenome hs37d5-cnv.graph.hla.rna-9-r3.0-1 9          
Homo sapiens [NCBI] hs37d5 Multigenome hs37d5+cnv+graph+rna-8-r1 8          
Linear reference Homo sapiens [NCBI] hs37d5 v4
hs37d5-cnv.hla.methylated_combined.rna-10-r4.0-1 10            
Homo sapiens [NCBI] hs37d5 v3 hs37d5-cnv.hla.rna-9-r3.0-1 9            

DRAGEN Resource Files

DRAGEN Component/Pipeline Resource Files Content Description  Size Date Major DRAGEN version
3.7 3.8 3.9 3.10 4.0 4.1 4.2 4.3
Illumina DRAGEN Hash Table Builder (Pangenome Generation) CHM13-v2 Multigenome Reference Collection v4 msVCF to build the DRAGEN multigenome reference, FASTA files, graph exclusion .bed files , mask .bed files, extra kmer .bed files (named "<FASTA>_graph_bed") Only use msVCF and graph exclusion .bed file to reconstruct the DRAGEN multigenome reference.
To customize the DRAGEN multigenome reference, use msVCF, and any of the other resource files.
  June 2024              
hg19 Multigenome Reference Collection v4                  
hg38 Multigenome Reference Collection v4                  
hs37d5 Multigenome Reference Collection v4 1.9 GB                
Illumina DRAGEN Output Reports DRAGEN Output Reports v4.3.6 Docker image in tar.gz Provides tools for generating rich, interactive and self-contained HTML reports from DRAGEN's output files 147 MB June 2024              
Illumina DRAGEN ML  DRAGEN ML Model v2.0 ML model file v2.0 To be used when DRAGEN ML is enabled during variant calling. For DRAGEN v4.0 and later, the ML model is packaged within DRAGEN. 13.7 GB      

1

1

1

1

1

DRAGEN ML Model v3.1 ML model file v3.1 13.7 GB        

1

1

1

1

Illumina DRAGEN Somatic small variant calling -  WGS, WES SNV Somatic Systematic Noise v2.0.0 Collection of noise baseline  BED  files for hg19, hs37d5, hg38 - WGS and WES To be used with DRAGEN small variant calling—Somatic 9.6 GB                
SNV Somatic Systematic Noise v1.1.0 1.5 GB              
Somatic Systematic Noise Baseline Collection v1.0.0 1.9 GB    
Illumina DRAGEN Somatic  SV calling -  WGS, WES SV Systematic Noise Baseline Collection v3.0.0 Collection of noise baseline BEDPE files for hg19, hs37d5, hg38, and Heme specific - WGS  To be used with DRAGEN SV calling—Somatic 112 MB May 2024              
SV Systematic Noise Baseline Collection v2.0.1 20.6 MB July 2023              
SV Systematic Noise Baseline Collection v1.0.0 16 MB Jul 2022            
Illumina DRAGEN CNV - Germline Enrichment pipelines CNV Panel of Normals for Twist Bioscience for Illumina Exome 2.5 Panel - DRAGEN 4.3 v1.0 Collection of panel of normals (PON) files (combined.counts.txt.gz) for exome PON generated from 54 samples, Illumina DNA Prep with Enrichment protocol, pooled by mass, overnight hybridization, sequencing on NovaSeq 6000 and NextSeq 2000. 4.4 GB June 2024              
CNV Panel of Normals for Twist Bioscience for Illumina Exome 2.5 Panel - DRAGEN 4.2 v2.0 PON generated from 54 samples, Illumina DNA Prep with Enrichment protocol, pooled by mass, overnight hybridization, sequencing on NextSeq 2000 only. 2.8 GB                
CNV Panel of Normals for Twist Bioscience for Illumina Exome 2.5 Panel - DRAGEN 4.2 v1.0 PON generated from 26 samples, Illumina DNA Prep with Exome 2.5 Enrichment protocol, pooled by volume, overnight hybridization, sequencing on NovaSeq 6000 only. 1.1 GB                
CNV Panel of Normals for Twist Bioscience for Illumina Exome 2.5 Panel - DRAGEN 4.0 v1.0 PON generated from 26 samples, Illumina DNA Prep with Exome 2.5 Enrichment protocol, pooled by volume, overnight hybridization, sequencing on NovaSeq 6000 only. 1.0 GB                
CNV Panel of Normals for Twist Bioscience for Illumina Exome 2.5 Panel - DRAGEN 3.10 v1.0 PON generated from 54 samples, Illumina DNA Prep with Enrichment protocol, pooled by mass, overnight hybridization, sequencing on NextSeq 2000 only. 914.9 MB                
                       
CNV Panel of Normals for TruSight Hereditary Cancer Panel - DRAGEN 4.3 v2.0

Collection of panel of normals files (PON) (combined.counts.txt.gz) for TruSight Hereditary Cancer Panel.

These are pre-constructed PON files. For optimal performance, it is recommended that you generate your own PON best matched to your lab's protocol.

PONs generated from 42 samples, Illumina DNA Prep with Enrichment protocol, hybridization at 58C, sequencing on MiSeq, NextSeq 550, NextSeq 2000, and NovaSeq 6000 41.8 MB                
CNV Panel of Normals for TruSight Hereditary Cancer Panel - DRAGEN 4.2 v1.0 30.2 MB                
Illumina DRAGEN CNV - Somatic TO (tumor-only) hg38 CNV Population SNP VCF v1.0 Collection of population SNPs used in tumor-only workflow To be used in tumor-only workflows to identify candidate germline heterozygous sites used to estimate B-allele profile in tumor samples 1.8 GB  
hg19 CNV Population SNP VCF v1.0 1.8 GB  
hs37d5 CNV population SNP VCF v1.0 1.8 GB  
CHM13-v2 CNV population SNP VCF v1.0 1.8 GB              
Illumina DRAGEN MSI Microsatellite Files v1.0.0 Collection of DRAGEN microsatellite site files To be used in DRAGEN WES / WGS somatic pipeline.   May 2024
Illumina DRAGEN SNV Pipeline Bed File Collection v1.0.0  Collection of ALU excluded region bed files for hg38, hg19 and hs37d5 ALU Bed files for use in FFPE samples with option --vc-excluded-regions-bed
  May 2024
Illumina DRAGEN MRJD DRAGEN MRJD utility software v1.0 A tar.gz file that includes readme, a python script, an MRJD region bed file, and a test dataset A utility software that replaces the DRAGEN Small Variant Caller output in the homology region of the six medically relevant and challenging genes with MRJD caller output 115 KB                  
Illumina DRAGEN Population Haplotyping  hg38 Genetic Map v2.0 Genetic map for autosomes and chr X, Genetic map configuration file
To be used with the Population Haplotyping tool to phase population datasets and infer haplotypes. The output builds a reference panel that can be used for Imputation. 22.4 MB Jul 2023            
Illumina DRAGEN Imputation  Imputation Reference Panel-IRPv2.1 Reference panel, genetic map, configuration files, and variant sites files  This reference panel contains autosomes and chrX, multiallelic SNPs, Indels, ~ 125M variants             

2

2

Imputation Reference Panel-IRPv2.0 This reference panel contains autosomes and chrX, multiallelic SNPs, Indels (<3% AF removed), ~ 110M variants  18.5 GB Jan 2024        

2

2

Imputation Reference Panel-IRPv1.2 This reference panel contains autosomes, bi-allelic SNPs, ~ 50M variants  8.2 GB Jul 2023        
Illumina DRAGEN Hash Table Builder CHM13-v2 Custom Multigenome Reference Collection v1.1.0 FASTA reference files, mask .bed files, graph .bed files

To be used only to build a custom multigenome reference for DRAGEN v.4.0, DRAGEN v.4.1 and DRAGEN v4.2.

Note: The DRAGEN multigenome reference cannot be reconstructed with these resource files.

1.1 GB Jul 2023              
hg19 Custom Multigenome Reference Collection v1.1.0 1.0 GB Jul 2023              
hg38 Custom Multigenome Reference Collection v1.1.0 1.0 GB Jul 2023              
hs37d5 Custom Multigenome Reference Collection v1.1.0 968 MB Jul 2023              
hg19 Custom Multigenome Reference Collection v1.0.0 3.2 GB Jul 2023            
hg38 Custom Multigenome Reference Collection v1.0.0 3.2 GB Jul 2023            
hs37d5 Custom Multigenome Reference Collection v1.0.0 3.2 GB Jul 2023            
Illumina DRAGEN ORA compression ORA Compression Reference files for human data  Reference and index files Compression with optimized DRAGEN ORA (v3.10 or later)- regular human data 2 GB Mar 2022      
ORA Compression Reference files for human data Compression of regular human data 1.5 GB Apr 2021  
ORA Compression Reference files for human bisulfite data  Compression of human bisulfite data (methylated DNA use case) 5 GB                
ORA Compression Reference files for other than human data Database with reference and index files to compress data other than human Refer to the following rows to download specific species resource files 26 GB                
          3.7 3.8 3.9 3.10 4.0 4.1 4.2 4.3
ORA Compression Reference files for pig data Sus scrofa 2 GB                
ORA Compression Reference files for chicken data Gallus gallus  981 MB                
ORA Compression Reference files for rice data Oryza sativa  315 MB                
ORA Compression Reference files for arabidopsis data Arabidopsis thaliana  110 MB                
ORA Compression Reference files for wheat data Triticum aestivum 6.2 GB                
ORA Compression Reference files for cattle data Bos taurus                  
ORA Compression Reference files for soybean data Glycine max                  
ORA Compression Reference files for rat data Rattus norvegicus 2 GB                
ORA Compression Reference files for maize data Zea may 1 GB                
ORA Compression Reference files for zebrafish data Danio rerio 1.2 GB                
ORA Compression Reference files for mouse data Mus musculus                  
ORA Compression Reference files for roundworm data Caenorhabditis elegans 92 MB                
ORA Compression Reference files for duck data Cairina moschata 1.0 GB                

1—Included in the DRAGEN installation

2—Compatible with DRAGEN v4.0 and v4.1 but there is no imputation on chX