DRAGEN

DRAGEN Images

The platform provides a set of cloud-enabled DRAGEN images, usable from Tools and task runs, via an AWS ECR. The following table includes the supported DRAGEN images.

📘 License Information

The images below indicated as "License Included" include a built-in DRAGEN license for use on ICA. The license information is stored at /opt/instance-identity within the container. The dragen application must include the --lic-instance-id-location option to point to the license file.

--lic-instance-id-location /opt/instance-identity

For images without the included license, the license information must be provided using the --lic-server option.

--lic-server user:[e-mail]

DRAGEN Version	Image	License Included
3.7.5	699120554104.dkr.ecr.us-east-1.amazonaws.com/public/dragen-byolic:3.7.5	No
3.7.5	699120554104.dkr.ecr.us-east-1.amazonaws.com/public/dragen:3.7.5	Yes
3.6.3	699120554104.dkr.ecr.us-east-1.amazonaws.com/public/dragen:3.6.3	Yes
3.5.7	699120554104.dkr.ecr.us-east-1.amazonaws.com/public/dragen:3.5.7	Yes
3.4.12	699120554104.dkr.ecr.us-east-1.amazonaws.com/public/dragen:3.4.12	Yes
3.4.9	699120554104.dkr.ecr.us-east-1.amazonaws.com/public/dragen:3.4.9	Yes
3.4.5	699120554104.dkr.ecr.us-east-1.amazonaws.com/public/dragen:3.4.5	Yes
3.4.3	699120554104.dkr.ecr.us-east-1.amazonaws.com/public/dragen:3.4.3	Yes
3.3.9	699120554104.dkr.ecr.us-east-1.amazonaws.com/public/dragen:3.3.9	Yes
3.3.7	699120554104.dkr.ecr.us-east-1.amazonaws.com/public/dragen:3.3.7	Yes

The DRAGEN application is located at /opt/edico/bin/dragen in the DRAGEN images.

Running DRAGEN on the platform using the above images requires executing preparation commands to enable the execution of the dragen application on cloud FPGA hardware.

• --partial-reconfig DNA-MAPPER or --partial-reconfig HMM

• --ignore-version-check true

/opt/edico/bin/dragen --partial-reconfig HMM --ignore-version-check true

When executing dragen, the /ephemeral mounted volume should be used for extracting and storing reference files and storing intermediate results for optimal performance. Prior to calling dragen to perform analysis, a subdirectory for the decompressed reference data should be created and the reference data should be extracted. In the example below, the hg19 reference tarball input is mounted to mount/index/hg19/hg19-cnv-anchored.v8.tar.

mkdir -p /ephemeral/ref
tar -C /ephemeral/ref -xvf /mount/index/hg19/hg19-cnv-anchored.v8.tar

When calling dragen to perform the analysis, the following options should be included:

• --intermediate-results-dir /ephemeral

• --ref-dir /ephemeral/ref

To put it all together, the following example demonstrates all the commands to include in a single dragen step (simplified to highlight the information above).

/opt/edico/bin/dragen --partial-reconfig HMM --ignore-version-check true; \
mkdir -p /ephemeral/ref; \
tar -C /ephemeral/ref -xvf /mount/index/hg19/hg19-cnv-anchored.v8.tar; \
/opt/edico/bin/dragen --intermediate-results-dir /ephemeral --ref-dir /ephemeral/ref ...

References and Hash Tables for Use With DRAGEN

v8 Hash Tables

DRAGEN versions 3.5.0 and later require v8 Hash Tables

Species	Region	Hash Version	GDS Location
A. Thalinana	use1, aps2, cac1, euc1	v8	gds://ilmn-reference-genomes/A_Thaliana.tar.gz?tenantId=YXdzLXVzLXBsYXRmb3JtOjEwMDAwNDIwOjY4MWVkZmM4LWI1ODYtNGEzMi05MmNmLTkwMmIxN2M3YjViZA
Bacillus cereus	use1, aps2, cac1, euc1	v8	gds://ilmn-reference-genomes/Bacillus_cereus_ATCC_10987.tar.gz?tenantId=YXdzLXVzLXBsYXRmb3JtOjEwMDAwNDIwOjY4MWVkZmM4LWI1ODYtNGEzMi05MmNmLTkwMmIxN2M3YjViZA
Rhodobacter sphaeroides	use1, aps2, cac1, euc1	v8	gds://ilmn-reference-genomes/Rhodobacter_sphaeroides_2.4.1.tar.gz?tenantId=YXdzLXVzLXBsYXRmb3JtOjEwMDAwNDIwOjY4MWVkZmM4LWI1ODYtNGEzMi05MmNmLTkwMmIxN2M3YjViZA
	use1, aps2, cac1, euc1	v8	gds://ilmn-reference-genomes//Rhodobacter_sphaeroides_2.4.1_12905.tar.gz?tenantId=YXdzLXVzLXBsYXRmb3JtOjEwMDAwNDIwOjY4MWVkZmM4LWI1ODYtNGEzMi05MmNmLTkwMmIxN2M3YjViZA
Caenorhabditis elegans	use1, aps2, cac1, euc1	v8	gds://ilmn-reference-genomes/WBcel235.tar.gz?tenantId=YXdzLXVzLXBsYXRmb3JtOjEwMDAwNDIwOjY4MWVkZmM4LWI1ODYtNGEzMi05MmNmLTkwMmIxN2M3YjViZA
Danio rerio	use1, aps2, cac1, euc1	v8	gds://ilmn-reference-genomes/Zebrafish_JQCY02.tar.gz?tenantId=YXdzLXVzLXBsYXRmb3JtOjEwMDAwNDIwOjY4MWVkZmM4LWI1ODYtNGEzMi05MmNmLTkwMmIxN2M3YjViZA
Escherichia coli	use1, aps2, cac1, euc1	v8	gds://ilmn-reference-genomes/eschColi_K12_1.tar.gz?tenantId=YXdzLXVzLXBsYXRmb3JtOjEwMDAwNDIwOjY4MWVkZmM4LWI1ODYtNGEzMi05MmNmLTkwMmIxN2M3YjViZA
Homo sapiens	use1, aps2, cac1, euc1	v8	gds://ilmn-reference-genomes/hg19_alt_aware.tar.gz?tenantId=YXdzLXVzLXBsYXRmb3JtOjEwMDAwNDIwOjY4MWVkZmM4LWI1ODYtNGEzMi05MmNmLTkwMmIxN2M3YjViZA
Homo sapiens	use1, aps2, cac1, euc1	v8	gds://ilmn-reference-genomes/hg19_no_alt_haps_no_decoys.tar.gz?tenantId=YXdzLXVzLXBsYXRmb3JtOjEwMDAwNDIwOjY4MWVkZmM4LWI1ODYtNGEzMi05MmNmLTkwMmIxN2M3YjViZA
Homo sapiens	use1, aps2, cac1, euc1	v8	https://s3.amazonaws.com/use1-prd-seq-hub-appdata/Edico_v8/hg19-cnv-anchored.v8.tar
Homo sapiens	use1, aps2, cac1, euc1	v8	https://s3.amazonaws.com/use1-prd-seq-hub-appdata/Edico_v8/hg19_no_alt_haps_no_decoys-cnv-anchored.v8.tar
Homo sapiens	use1, aps2, cac1, euc1	v8	https://s3.amazonaws.com/use1-prd-seq-hub-appdata/Edico_v8/GRCh37-cnv-anchored.v8.tar
Homo sapiens	use1, aps2, cac1, euc1	v8	https://s3.amazonaws.com/use1-prd-seq-hub-appdata/Edico_v8/hs37d5-cnv-anchored.v8.tar
Homo sapiens	use1, aps2, cac1, euc1	v8	https://s3.amazonaws.com/use1-prd-seq-hub-appdata/Edico_v8/hg38_altaware-cnv-anchored.v8.tar
Homo sapiens	use1, aps2, cac1, euc1	v8	https://s3.amazonaws.com/use1-prd-seq-hub-appdata/Edico_v8/hg38_altaware_nohla-cnv-anchored.v8.tar
Homo sapiens	use1, aps2, cac1, euc1	v8	https://s3.amazonaws.com/use1-prd-seq-hub-appdata/Edico_v8/hg38_noalt_with_decoy-cnv-anchored.v8.tar
Mus musculus	use1, aps2, cac1, euc1	v8	gds://ilmn-reference-genomes/mm10.tar.gz?tenantId=YXdzLXVzLXBsYXRmb3JtOjEwMDAwNDIwOjY4MWVkZmM4LWI1ODYtNGEzMi05MmNmLTkwMmIxN2M3YjViZA
Escherichia virus ΦX174	use1, aps2, cac1, euc1	v8	gds://ilmn-reference-genomes/phix.tar.gz?tenantId=YXdzLXVzLXBsYXRmb3JtOjEwMDAwNDIwOjY4MWVkZmM4LWI1ODYtNGEzMi05MmNmLTkwMmIxN2M3YjViZA
Rattus norvegicus	use1, aps2, cac1, euc1	v8	gds://ilmn-reference-genomes/rn6.tar.gz?tenantId=YXdzLXVzLXBsYXRmb3JtOjEwMDAwNDIwOjY4MWVkZmM4LWI1ODYtNGEzMi05MmNmLTkwMmIxN2M3YjViZA

v7 Hash Tables

Species	Hash Version	GDS Location
Homo sapiens	v7	https://stratus-documentation-us-east-1-public.s3.amazonaws.com/dragen/reference/Homo_sapiens/grch37-cnv-anchored.v7.tar
	v7	https://stratus-documentation-us-east-1-public.s3.amazonaws.com/dragen/reference/Homo_sapiens/hg19-cnv-anchored.v7.tar
	v7	https://stratus-documentation-us-east-1-public.s3.amazonaws.com/dragen/reference/Homo_sapiens/hg38_altaware-cnv-anchored.v7.tar
	v7	https://stratus-documentation-us-east-1-public.s3.amazonaws.com/dragen/reference/Homo_sapiens/hg38_altaware_nohla-cnv-anchored.v7.tar
	v7	https://stratus-documentation-us-east-1-public.s3.amazonaws.com/dragen/reference/Homo_sapiens/hs37d5-cnv-anchored.v7.tar