| Assembly | Type | Reference Genome Hash Table | File Name | Major DRAGEN Version | 3.8 | 3.9 | 3.10 | 4.0 | 4.2 | 4.3 | 4.4 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Hash Table Version | 8 | 8 | 8 | 8 | 9 | 10 | 11 | |||||
| CHM13 | Pangenome (Graph) reference | Homo sapiens [T2T] CHM13_v2 v5 Pangenome | chm13_v2-cnv.graph.hla.methyl_cg.rna-11-r5.0-1 | 11 | ✓ | |||||||
| 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 v5 | chm13_v2-cnv.hla.methyl_cg.methylated_combined.rna-11-r5.0-1 | 11 | ✓ | ||||||||
| 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 | Pangenome (Graph) reference | Homo sapiens [UCSC] hg19 v5 Pangenome | hg19-alt_masked.cnv.graph.hla.methyl_cg.rna-11-r5.0-1 | 11 | ✓ | |||||||
| 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 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 v5 | hg19-alt_masked.cnv.hla.methyl_cg.methylated_combined.rna-11-r5.0-1 | 11 | ✓ | ||||||||
| Homo Sapiens [UCSC] hg19 v4 | hg19-alt_masked.cnv.hla.methylated_combined.rna-10-r4.0-1 |
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 | Pangenome (Graph) reference | Homo sapiens [1000 Genomes] hg38 v5 Pangenome | hg38-alt_masked.cnv.graph.hla.methyl_cg.rna-11-r5.0-1 | 11 | ✓ | |||||||
| 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 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 v5 | hg38-alt_masked.cnv.hla.methyl_cg.methylated_combined.rna-11-r5.0-1 | 11 | ✓ | ||||||||
| 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 | Pangenome (Graph) reference | Homo sapiens [NCBI] hs37d5 v5 Pangenome | hs37d5-cnv.graph.hla.methyl_cg.rna-11-r5.0-1 | 11 | ✓ | |||||||
| Homo sapiens [NCBI] hs37d5_chr v5 Pangenome | hs37d5_chr-cnv.graph.hla.methyl_cg.rna-11-r5.0-1 | 11 | ✓ | |||||||||
| 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 v5 | hs37d5-cnv.hla.methyl_cg.methylated_combined.rna-11-r5.0-1 | 11 | ✓ | ||||||||
| Homo sapiens [NCBI] hs37d5_chr v5 | hs37d5_chr-cnv.hla.methyl_cg.methylated_combined.rna-11-r5.0-1 | 11 | ✓ | |||||||||
| 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 | ✓ | |||||||||
| hg38-mm39 | Linear reference | Homo sapiens [1000 Genomes] - Mus musculus [Gencode] - hg38-mm39 v5 | hg38-mm39-alt_masked.cnv.hla.methyl_cg.methylated_combined.rna-11-r5.0-1 | 11 | ✓ |
| 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 | 4.4 | ||||||
| Illumina DRAGEN Hash Table Builder (Pangenome Reference Generation) | CHM13-v2 Pangenome Reference Collection v5 | msVCF to build the DRAGEN multigenome reference, FASTA files, graph exclusion .bed files , mask .bed files, extra kmer .bed files (named "<FASTA>_graph_bed") | To reconstruct the DRAGEN multigenome reference use all the files provided from same the reference build. To customize the DRAGEN multigenome reference, use msVCF, and any of the other resource files. |
2.3 GB | May 2025 | ✓ | ||||||||
| hg19 Pangenome Reference Collection v5 | 2.1 GB | ✓ | ||||||||||||
| hg38 Pangenome Reference Collection v5 | 2.1 GB | ✓ | ||||||||||||
| hs37d5 Pangenome Reference Collection v5 | 2.1 GB | ✓ | ||||||||||||
| CHM13-v2 Multigenome Reference Collection v4 | 2.1 GB | June 2024 | ✓ | |||||||||||
| hg19 Multigenome Reference Collection v4 | 2.0 GB | ✓ | ||||||||||||
| hg38 Multigenome Reference Collection v4 | 2.0 GB | ✓ | ||||||||||||
| hs37d5 Multigenome Reference Collection v4 | 1.9 GB | ✓ | ||||||||||||
| Illumina DRAGEN Output Reports | DRAGEN Output Reports rpm v4.4.4 - Reports | Docker image or rpm package in tar.gz | Provides tools for generating rich, interactive and self-contained HTML reports from DRAGEN's output files. Summary report is a summary of main metrics vs. full report. | 33 B | May 2025 | ✓ | ||||||||
| DRAGEN Output Reports rpm v4.4.4 - Summary Reports | 14 MB | ✓ | ||||||||||||
| DRAGEN Output Reports v4.3.6 | 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 |
1 | |||
| DRAGEN ML Model v3.1 | ML model file v3.1 | 13.7 GB | ✓ | 1 |
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 v3.1.0 | Collection of noise baseline BEDPE files for hg19, hs37d5, hs37d5-chr, hg38, WGS, and FFPE sample/Heme specific | To be used with DRAGEN SV calling—Somatic | 185 MB | May 2025 | ✓ | ||||||||
| SV Systematic Noise Baseline Collection v3.0.0 | Collection of noise baseline BEDPE files for hg19, hs37d5, hg38, WGS and Heme specific | 112 MB | May 2024 | ✓ | ||||||||||
| SV Systematic Noise Baseline Collection v2.0.1 | Collection of noise baseline BEDPE files for hg19, hs37d5, hg38 - WGS and WES | 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 FFPE 2.5 - DRAGEN 4.4 v1.0 | PON generated from 45 FFPE benign adjacent samples from different tissue types with Illumina FFPE DNA Prep with Exome 2.5 Enrichment protocol and sequenced on the NovaSeq 6000. | 404 MB | May 2025 | ✓ | |||||||||
| CNV Panel of Normals for Twist Bioscience for Illumina Exome Mito 2.5 - DRAGEN 4.4 v1.0 | PON generated from 54 samples, Illumina DNA Prep with Enrichment protocol with mitochondrial genome enrichment, pooled by mass, overnight hybridization, sequencing on NovaSeq 6000 and NextSeq 2000 | 1.9 GB | May 2025 | ✓ | ||||||||||
| CNV Panel of Normals for Twist Bioscience for Illumina Exome 2.5 - DRAGEN 4.4 v1.0 | PON generated from 54 samples, Illumina DNA Prep with Enrichment protocol, pooled by mass, overnight hybridization, sequencing on NovaSeq 6000 and NextSeq 2000 | 1.9 GB | May 2025 | ✓ | ||||||||||
| 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 4.4 v1.0 | 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 | 34 MB | May 2025 | ✓ | |||||||||
| CNV Panel of Normals for TruSight Hereditary Cancer Panel - DRAGEN 4.3 v2.0 | 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) and Illumina DRAGEN Germline ASCN CNV |
hg38 CNV Population SNP VCF v1.0 | Collection of population SNPs used in tumor-only workflow for Somatic pipeline, and in ASCN CNV Germline pipeline | To be used in tumor-only workflows to identify candidate germline heterozygous sites used to estimate B-allele profile in tumor samples. To be used in germline ASCN workflows to identify candidate sites used to estimate B-allele profile in germline samples. |
1.8 GB | S | S | S | S | S | S | S | S | S and G | |
| hg19 CNV Population SNP VCF v1.0 | 1.8 GB | S | S | S | S | S | S | S | S | S and G | ||||
| hs37d5 CNV population SNP VCF v1.0 | 1.8 GB | S | S | S | S | S | S | S | S | S and G | ||||
| CHM13-v2 CNV population SNP VCF v1.0 | 4.0 GB | S | S | S and G | ||||||||||
| Illumina DRAGEN MSI | Microsatellite Files v1.1.0 | Collection of DRAGEN Microsatellite Site Files to be used in DRAGEN WES / WGS somatic pipeline. | This version adds panel of normal for FFPE samples WGS/WES, MSI sites have been further curated. Recommendation is to use this version for v4.2+. | 385 MB | May 2025 | ✓ | ✓ | ✓ | ||||||
| Microsatellite Files v1.0.0 | 48 MB | 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 |
37 MB | May 2024 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| Illumina DRAGEN Targeted caller | Targeted Caller Systematic Noise Baseline Collection v1.0.0 | Collection of systematic noise baseline json files for hg38, hg19 and hs37d5 | To be used with targeted caller on WES data. | 138 MB | May 2025 | ✓ | ||||||||
| 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 scRNA, CRISPR, scATAC Illumina DRAGEN Bulk RNA |
Gene annotation files collection v1.0 | Versions of GTF gene annotations downloaded from https://www.gencodegenes.org/ for use with the corresponding genome assembly: hg38, hg19, hs37d5, hs37d5-chr, hg38-mm39 Each annotation contains the comprehensive gene annotation on the reference chromosomes only (excluding scaffolds, assembly patches and alternate loci). |
Gene annotation input used for validation and benchmarking of the indicated version of DRAGEN software. gencode_hs37d5_chr.v19.annotation.gtf tested for bulk RNA pipeline gencode.hg38_v44.mm39_vM30.annotation.gtf.gz tested for scRNA pipeline only gencode.v44.annotation.gtf.gz, gencode.v19.annotation.gtf tested for all pipelines. You may use a different annotation on an "as needed" basis at your discretion (eg, different assemblies or species). |
283 MB | May 2025 | For earlier versions, contact Illumina Technical Support. | ✓ | ✓ | ✓ | |||||
| 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 | 20 GB | June 2024 | 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 | June 2024 | ✓ | ✓ | |||||||||
| Database with all species supported, V2 adds the Duck reference vs. the previous version | Refer to the following rows to download specific species resource files | 27 GB | May 2025 | ✓ | ✓ | |||||||||
| 3.7 | 3.8 | 3.9 | 3.10 | 4.0 | 4.1 | 4.2 | 4.3 | 4.4 | ||||||
| ORA Compression Reference files for pig data | Sus scrofa | 2 GB | ✓ | ✓ | ||||||||||
| ORA Compression Reference files for chicken data | Gallus gallus | 986 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 | 2 GB | ✓ | ✓ | ||||||||||
| ORA Compression Reference files for soybean data | Glycine max | 685 MB | ✓ | ✓ | ||||||||||
| 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 | 2 GB | ✓ | ✓ | ||||||||||
| 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 installer
2—Compatible with DRAGEN v4.0 and v4.1 but there is no imputation on chX
S—Available for the somatic pipeline
S and G—Available for the somatic and germline pipelines