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 v2.0.0 | 21.2 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 3.10 | Collection of panel of normals files (combined.counts.txt.gz) for Exome | To be used for WES in the DRAGEN CNV pipeline. These are pre-constructed panel of normals files that can be used in DRAGEN CNV WES workflows. For optimal performance, Illumina recommends that you generate your own panel of normals best matched to your lab's protocol. | 0.9 GB | June 2024 | ✓ | |||||||
| CNV Panel of Normals for Twist Bioscience for Illumina Exome 2.5 Panel - DRAGEN 4.0 | 1.0 GB | ✓ | ✓ | ||||||||||
| CNV Panel of Normals for Twist Bioscience for Illumina Exome 2.5 Panel - DRAGEN 4.2 | 1.1 GB | ✓ | |||||||||||
| CNV Panel of Normals for Twist Bioscience for Illumina Exome 2.5 Panel - DRAGEN 4.3 | 4.4 GB | ✓ | ✓ | ||||||||||
| CNV Panel of Normals for TruSight Hereditary Cancer Panel - DRAGEN 4.2 | 30.2 MB | ✓ | |||||||||||
| CNV Panel of Normals for TruSight Hereditary Cancer Panel - DRAGEN 4.3 | 41.8 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, a 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, 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 methylated 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 | ✓ | ||||||||||
1—Included in the DRAGEN installation
2—Compatible with DRAGEN v4.0 and v4.1 but there is no imputation on chX