Supported reference genome assemblies

Both GRCh37/hg19 and GRCh38/hg38 are supported. You can run cases with both reference genomes in the same organization.

Note: Curated and historical data are automatically lifted over on the fly.

For the DRAGEN v4.3 analysis, Emedgene utilizes:

• GRCh38/hg38: Multigenome Graph hg38-alt_masked.cnv.graph.hla.rna-10-r4.0-1.tar.gz.

  Pre-built multigenome hash tables for hg38. The hash table builds include DNA, RNA, CNV, and HLA tables. Download here.

• GRCh37d5: Multigenome Graph hs37d5-cnv.graph.hla.rna-10-r4.0-1.tar.gz.

  Pre-built multigenome hash tables for GRCh37d5. The hash table builds include DNA, RNA, CNV, and HLA tables. Download here.

For the DRAGEN v4.2 analysis, Emedgene utilizes:

• GRCh38/hg38: Multigenome Graph hg38-alt_masked.cnv.graph.hla.rna-9-r3.0.tar.gz. Pre-built multigenome hash tables for hg38. The hash table builds include DNA, RNA, CNV, and HLA tables. Download here.

• GRCh37d5: Multigenome Graph hs37d5-cnv.graph.hla.rna-9-r3.0.tar.gz.

  Pre-built multigenome hash tables for GRCh37d5. The hash table builds include DNA, RNA, CNV, and HLA tables. Download here.

For the DRAGEN v4.0 analysis, Emedgene utilizes:

• GRCh38/hg38: Multigenome Graph hg38-alt_masked.cnv.graph.hla.rna-8-r2.0-1.tar.gz.

  Pre-built multigenome hash tables for hg38. The hash table builds include DNA, RNA, CNV, and HLA tables. Download here.

• GRCh37d5: Multigenome Graph hs37d5-cnv.graph.hla.rna.tar.gz.

  Pre-built multigenome hash tables for GRCh37d5. The hash table builds include DNA, RNA, CNV, and HLA tables. Available on demand.

For DRAGEN versions < 4.0, Emedgene utilizes:

• GRCh38/hg38: GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz.

  Contains the sequences of the chromosomes, the rCRS mitochondrial sequence, unlocalized scaffolds, and unplaced scaffolds. Download here.

• GRCh37/hg19: hs37d5.fa.gz. Includes data from GRCh37, the rCRS mitochondrial sequence, Human herpesvirus 4 type 1 and the concatenated decoy sequences. Download here.

Demystifying the versions of GRCh38/hg38 reference genomes, how they are used in DRAGEN and their impact on accuracywww.illumina.com