DRAGEN Product Obsolescence Notices
DRAGEN Secondary Analysis - End of Life Roadmap
This section refers to DRAGEN Secondary Analysis package versions for use on-prem and BYOL
v3.3 and lower
June 1, 2025
v3.9 and lower*
December 1, 2025
v3.10 and lower*
June 1, 2026
*v3.7.8 and v3.9.5 will continue to be supported by Illumina indefinitely
After the dates of obsolescence, there will be no further updates, improvements, bug fixes, or support for the affected versions. Customers will no longer have access to download installers, release notes, and user guides after date of obsolescence.
DRAGEN BSSH/ICA Workflows - End of Life Roadmap
The DRAGEN Support Team strongly recommends transitioning to F2 enabled workflows by November 20, 2025 to ensure a smooth transition and minimize analysis delays as F1 instances are taken offline.
Amazon Web Services’ announcement in 2024 that their F1 instances will be replaced by a new generation of FPGA-powered cloud hardware, Amazon EC2 F2 instances, throughout 2025. F1 instances will be phased out of service and made obsolete by December 20, 2025.
DRAGEN pipelines on ICA and BSSH make use of these F instances to run FPGA-accelerated DRAGEN analysis workflows in the cloud. To ensure uninterrupted service, Illumina is releasing updated versions of DRAGEN pipelines compatible with F2 instances within the same time frame. This change impacts all DRAGEN pipelines before v4.4.4. In addition to having ongoing AWS support, F2 instances introduce capacity and performance improvements with up to 40% reduced turnaround time for analysis (runtime and queue times).
F2-compatible DRAGEN versions of BSSH and ICA apps are being made available for a subset of current versions (see tables below). Upgrade pathways described in Tables 1 and 2 will produce read, variant, and metric exact results on F2 instances.
The transition from F1 to F2 will be accompanied by pricing changes for BSSH and ICA. DRAGEN pipelines running on F2 will incur the following DRAGEN License cost per gigabase of data processed in addition to an hourly F-instance computer cost.
<=80
0.10
>80 and <=160
0.08
>160 and <=240
0.07
>240 and <=320
0.06
>320
0.05
Note: If your DRAGEN job fails, no DRAGEN license cost will be charged.
F2 Regional Availability
Australia - Sydney
AU
Yes
Canada - Central
CA
Yes
Germany - Frankfurt
EU
Yes
India - Mumbai
IN
Yes
Indonesia - Jakarta
ID
No*
Israel - Tel Aviv
IL
No*
Japan - Tokyo
JP
Yes
South Korea - Seoul
KR
No*
Singapore
SG
Yes
United Arab Emirates
AE
No*
United Kingdom - London
GB
Yes
N. Virginia
US
Yes
*We are coordinating with our underlying cloud provider and will share updates to this page as they become available
Table 1, ICA workflows + F2 patched versions
DRAGEN Amplicon DNA and RNA 4-2-4-v2
DRAGEN_Amplicon_DNA_and_RNA_4-2-4-2
Available now
DRAGEN Amplicon DNA and RNA 4-3-6
DRAGEN_Amplicon_DNA_and_RNA_4-3-6-1
Available now
DRAGEN CNV Baseline Builder 4-2-4-v2
DRAGEN_CNV_Baseline_Builder_4-2-4-2
Available now
DRAGEN CNV Baseline Builder 4-3-6
DRAGEN_CNV_Baseline_Builder_4-3-6-1
Available now
DRAGEN Germline Whole Genome 4-2-4-v2
DRAGEN_Germline_Whole_Genome_4-2-4-2
Available now
DRAGEN_Germline_Whole_Genome_4-3-6_v2
DRAGEN_Germline_Whole_Genome_4-3-6-1
Available now
DRAGEN_Germline_Whole_Genome_4-3-13
DRAGEN_Germline_Whole_Genome_4-3-13-1
Available now
DRAGEN Germline Enrichment 4-2-4-v2
DRAGEN_Germline_Enrichment_4-2-4-2
Available now
DRAGEN Germline Enrichment 4-3-6
DRAGEN_Germline_Enrichment_4-3-6-1
Available now
DRAGEN_Germline_Enrichment_4-3-13
DRAGEN_Germline_Enrichment_4-3-13-1
Available now
DRAGEN for ILMN cfDNA Prep with Enrichment 4-0-3
DRAGEN_for_ILMN_cfDNA_Prep_with_Enrichment_4-0-3-1
Available now
DRAGEN Imputation 4-2-4
DRAGEN_Imputation_4-2-4-2
Available now
DRAGEN Imputation 4-2-7-v3
DRAGEN_Imputation_4-2-7-1
October 2025
DRAGEN Joint Pedigree Calling 4-2-4-v2
DRAGEN_Joint_Pedigree_4-2-4-2
Available now
DRAGEN Joint Pedigree Calling 4-3-6
DRAGEN_Joint_Pedigree_4-3-6-1
Available now
DRAGEN End to End Joint Pedigree Calling 4-2-7
DRAGEN_End-to-End_Joint_Pedigree_Calling_4-2-7-1
October 2025
DRAGEN End to End Joint Pedigree Calling 4-3-6
DRAGEN_End-to-End_Joint_Pedigree_Calling_4-3-6-1
Available now
DRAGEN_End-to-End_Joint_Pedigree_Calling_4-3-13
DRAGEN_End-to-End_Joint_Pedigree_Calling_4-3-13-1
Available now
DRAGEN Methylation 4-3-6
DRAGEN_Methylation_4-3-6-1
Available now
DRAGEN_Methylation_4-3-13
DRAGEN_Methylation_4-3-13-1
Available now
DRAGEN MSI Baseline Builder 4-3-6
DRAGEN_MSI_Baseline_Builder_4-3-6-1
Available now
DRAGEN_Multigenome_Reference_Builder_4-3-6
DRAGEN_Multigenome_Reference_Builder_4-3-6-1
October 2025
DRAGEN_Pangenome_VCF_Builder_4-3-6
DRAGEN Pangenome VCF Builder v4.4.x
October 2025
DRAGEN RNA 4-2-4-v2
DRAGEN_RNA_4-2-4-2
Available now
DRAGEN RNA 4-3-6
DRAGEN_RNA_4-3-6-1
Available now
DRAGEN_RNA_4-3-13
DRAGEN_RNA_4-3-13-1
Available now
DRAGEN_Small_WGS_4-3-13
DRAGEN_Small_WGS_4-3-13-1
Available now
DRAGEN Somatic Whole Genome 4-2-4-v2
DRAGEN_Somatic_Whole_Genome_4-2-4-2
Available now
DRAGEN Somatic Whole Genome 4-3-6
DRAGEN_Somatic_Whole_Genome_4-3-6-1
Available now
DRAGEN_Somatic_Whole_Genome_4-3-13
DRAGEN_Somatic_Whole_Genome_4-3-13-1
Available now
DRAGEN Somatic Enrichment 4-2-4-v2
DRAGEN_Somatic_Enrichment_4-2-4-2
Available now
DRAGEN Somatic Enrichment 4-3-6
DRAGEN_Somatic_Enrichment_4-3-6-1
Available now
DRAGEN_Somatic_Enrichment_4-3-13
DRAGEN_Somatic_Enrichment_4-3-13-1
Available now
DRAGEN Systematic Noise File Builder 4-2-4-v2
DRAGEN_Systematic_Noise_File_Builder_4-2-4-2
Available now
DRAGEN Systematic Noise File Builder 4-3-6
DRAGEN_Systematic_Noise_File_Builder_4-3-6-1
Available now
DRAGEN Reference Builder 4-2-4-v2
DRAGEN_Reference_Builder_4-2-4-2 (SW only mode)
Available now
DRAGEN Reference Builder 4-3-6
DRAGEN_Reference_Builder_4-3-6-1 (SW only mode)
Available now
Table 2, BSSH apps + F2 patched versions
DRAGEN Baseline Builder v4.2.4
DRAGEN Baseline Builder v4.2.4001
September 2025
DRAGEN Baseline Builder v4.3.6
DRAGEN Baseline Builder v4.3.6001
September 2025
DRAGEN Enrichment v4.2.4
DRAGEN Enrichment v4.2.4001
September 2025
DRAGEN Enrichment v4.2.7
DRAGEN Enrichment v4.2.7001
September 2025
DRAGEN Enrichment v4.3.6
DRAGEN Enrichment v4.3.6001
September 2025
DRAGEN Enrichment v4.3.13
DRAGEN Enrichment v4.3.13001
Available now
DRAGEN Germline v4.2.4
DRAGEN Germline v4.2.4001
September 2025
DRAGEN Germline v4.3.6
DRAGEN Germline v4.3.6001
Available now
DRAGEN Germline v4.3.13
DRAGEN Germline v4.3.13001
Available now
DRAGEN ILMN cfDNA Prep v4.0.3
DRAGEN ILMN cfDNA Prep v4.0.3001
Available now
DRAGEN Imputation v4.2.7
DRAGEN Imputation v4.2.7001
September 2025
DRAGEN Imputation v4.3.6
DRAGEN Imputation v4.3.6001
September 2025
DRAGEN Joint Genotyping v4.2.4
DRAGEN Joint Genotyping v4.2.4001
September 2025
DRAGEN Joint Genotyping v4.3.6
DRAGEN Joint Genotyping v4.3.6001
September 2025
DRAGEN Methylation v4.3.6
DRAGEN Methylation v4.3.6001
September 2025
DRAGEN Methylation v4.3.13
DRAGEN Methylation v4.3.13001
August 2025
DRAGEN Microbial Enrichment Plus v1.1.0
DRAGEN Microbial Enrichment Plus v1.1.1
Available now
DRAGEN Pangenome Reference Builder v4.3.6
DRAGEN Pangenome Reference Builder v4.3.6001
September 2025
DRAGEN Pangenome VCF Builder v4.3.6
DRAGEN Pangenome VCF Builder v4.3.6001
September 2025
DRAGEN Reference Builder v4.2.4
DRAGEN Reference Builder v4.2.4001
September 2025
DRAGEN Reference Builder v4.3.6
DRAGEN Reference Builder v4.3.6001
September 2025
DRAGEN small WGS v4.3.13
DRAGEN small WGS v4.3.13001
August 2025
DRAGEN Somatic v4.2.4
DRAGEN Somatic v4.2.4001
September 2025
DRAGEN Somatic v4.2.7
DRAGEN Somatic v4.2.7001
September 2025
DRAGEN Somatic v4.3.6
DRAGEN Somatic v4.3.6001
September 2025
DRAGEN Somatic v4.3.13
DRAGEN Somatic v4.3.13001
August 2025
Recommended transition paths for all other versions are summarized in tables 3 and 4 below. Applications using these transition paths are not receiving bit exact equivalent apps, and Illumina recommends upgrading to a more recent version of the release workflow when available. Because these upgrades use different underlying DRAGEN versions, the results will not have bit exact outputs.
Table 3, Recommended transition paths for all other DRAGEN ICA workflows using F1 instances
DRAGEN Amplicon v3.10.4, v4.0.3
DRAGEN Amplicon DNA + RNA v4.4.4
Available now
DRAGEN CNV Baseline Builder v3.10.4, v4.0.3
DRAGEN CNV Baseline Builder v4.4.4
Available now
DRAGEN FASTQC + MultiQC DRAGEN FASTQC/MultiQC v3.9.5
DRAGEN Germline WGS v4.4.4 (Map/Align provides the same functionality as this app)
Available now
DRAGEN Germline WGS v3.8.4, v3.9.5, v3.10.4, v3.10.8, v4.0.3, v4.0.5, v4.1.5, v4.1.23
DRAGEN Germline WGS v4.4.4
Available now
DRAGEN Germline Enrichment v3.9.5, v3.10.4, v3.10.8, v4.0.3, v4.1.5, v4.1.23
DRAGEN Germline Enrichment v4.4.4
Available now
DRAGEN Imputation v4.0.3
DRAGEN Imputation v4.2.7-1
October 2025
DRAGEN Joint Genotyping v3.9.5 DRAGEN Joint Pedigree v3.10.4, v4.0.5
DRAGEN Joint Pedigree v4.4.4
Available now
DRAGEN E2E Joint Pedigree v3.10.4, v4.0.3
DRAGEN E2E Joint Pedigree v4.4.4
Available now
DRAGEN Methylation v3.9.5, v3.10.4, v4.0.3, v4.1.23
DRAGEN Methylation v4.4.4
Available now
DRAGEN RNA v3.9.5, v3.10.4, v4.0.3, v4.1.5, v4.1.23
DRAGEN RNA v4.4.4
Available now
DRAGEN scRNA v3.9.5, v4.0.3
DRAGEN scRNA v4.4.x
October 2025
DRAGEN Somatic WGS v3.9.5, v3.10.4, v4.0.3, v4.0.5, v4.1.23
DRAGEN Somatic WGS v4.4.4
Available now
DRAGEN Somatic Enrichment v3.10.4, v4.0.3, v4.1.5, v4.1.23
DRAGEN Somatic Enrichment v4.4.4
Available now
DRAGEN Reference Builder v3.9.5, v3.10.4, v4.0.3
No alternative app planned. Recommend moving to newer v4.3/v4.4 workflows.
N/A
Table 4, Recommended transition paths for all other DRAGEN BSSH apps using F1 instances
DRAGEN Amplicon v3.8.6, v3.9.5, v3.10.4, v4.2.4, v4.3.6, v4.3.13
DRAGEN Amplicon v4.4.4
Available now
DRAGEN Baseline Builder v3.7.5, v3.8.4, v3.9.5, v3.10.4, v4.0.3, v4.1.23
DRAGEN Baseline Builder v4.4.4
Available now
DRAGEN Baseline Builder v4.3.7, v4.3.8
DRAGEN Baseline Builder v4.3.6001
September 2025
DRAGEN CNV Baseline Builder v3.4.5, v3.4.6, v3.5.7, v3.6.3
DRAGEN Baseline Builder v4.3.6001
September 2025
DRAGEN Enrichment v3.4.5, v3.5.7, v3.6.3, v3.7.5, v3.8.4, v3.9.5, v3.10.4, v4.0.3, v4.1.23
DRAGEN Enrichment v4.4.4
Available now
DRAGEN FASTQ Toolkit v1.0.0, v1.1.0, v1.2.0, v1.3.1
New app to be developed
2026
DRAGEN FASTQC + MultiQC v3.6.3, v3.9.5
DRAGEN Germline v4.4.4 (Map/Align only provides the same functionality as this app)
Available now
DRAGEN Germline v3.3.7, v3.4.5, v3.5.7, v3.6.3, v3.7.5, v3.8.4, v3.9.5, v3.10.4, v4.0.3, v4.1.23
DRAGEN Germline v4.4.4
Available now
DRAGEN Germline v4.3.7
DRAGEN Germline v4.3.6001
September 2025
DRAGEN Germline All Callers v3.9.5
DRAGEN Germline v4.4.4
Available now
DRAGEN Germline for Pop Gen v3.7.8
DRAGEN Germline v4.4.4
Available now
DRAGEN Imputation v4.0.3
DRAGEN Imputation v4.3.6001
September 2025
DRAGEN Joint Genotyping v3.2.8, v3.3.7, v3.4.5, v3.4.12, v3.5.7, v3.6.3, v3.7.5, v3.9.5, v3.10.4, v4.3.7
DRAGEN Joint Genotyping v4.3.6001
September 2025
DRAGEN Metagenomics Pipeline v3.5.8, v3.5.9, v3.5.10, v3.5.11, v3.5.12, v3.5.13
DRAGEN 16s Plus v1.0.0 Future shotgun sequencing app
16s Plus available now Future shotgun seq app availability TBD
DRAGEN PopGen v3.10.4, v3.10.5
DRAGEN PopGen v4.3.6
Available now
DRAGEN Reference Builder v3.2.8, v3.3.7, v3.4.5, v3.5.7, v3.6.3, v3.7.5, v3.8.4, v3.9.5, v3.10.4, v4.0.3, v4.1.23
DRAGEN Reference Builder v4.4.4
Available now
DRAGEN RNA v3.3.7, v3.4.5, v3.5.7, v3.6.3, v3.7.5, v3.8.4, v3.9.5, v3.10.4, v4.0.3, v4.0.4, v4.1.23, v4.2.4, v4.2.7, v4.3.6, v4.3.7, v4.3.13
DRAGEN RNA v4.4.4
Available now
DRAGEN scATAC v4.0.3, v4.2.4
End of life, no replacement planned
N/A
DRAGEN scRNA v3.7.4, v3.8.4, v3.9.5, v3.10.4, v4.0.3, v4.2.4, v4.3.6, v4.4.2
DRAGEN scRNA v4.4.x
October 2025
DRAGEN Somatic v3.2.8, v3.3.7, v3.4.5, v3.5.7, v3.6.3, v3.7.5, v3.8.4, v3.9.5, v3.10.4, v4.0.3, v4.1.23
DRAGEN Somatic v4.4.4
Available now
Reference Builder (Instrument) on BSSH v1.0.0, v1.1.0, v1.2.0, v2.0.0, v3.0.0
Reference Builder (Instrument) v4.4.x
2025
Information on TSO 500 and TSO 500 ctDNA F2 transition may be found in the TSO 500 Software User Guide.
BCL Convert BSSH Workflow End of Life Roadmap
Several versions of BCL Convert on BSSH will be obsolesced on December 20, 2025. These apps are not impacted by F instance migration but are being obsolesced as part of an ongoing effort to streamline our software products and portfolio.
Recommended transition paths for BCL Convert EOL versions
BCL Convert v1.2.0, v1.2.1, v1.3.0, v2.0.0, v2.1.0, v2.2.0, v2.3.0, v2.4.0 BCL EA v1.1.0 BCL for ICA Beta v1.0.0
BCL v2.7.0
Available now
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