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:password@license.edicogenome.com
DRAGEN VersionImageLicense 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

SpeciesRegionHash VersionGDS 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

SpeciesHash VersionGDS 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

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