| Configuration: CPU-equivalent GATK germline pipeline on a CPU node (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 60h Runtime (Germline FASTQ to VCF; human WGS at 100x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCPU-equivalent GATK germline pipeline on a CPU node, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 100x, column 'CPU' |
|---|
| Configuration: CPU-equivalent GATK germline pipeline on a CPU node (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 17h Runtime (Germline FASTQ to VCF; human WGS at 30x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCPU-equivalent GATK germline pipeline on a CPU node, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 30x, column 'CPU' |
|---|
| Configuration: CPU-equivalent GATK germline pipeline on a CPU node (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 24h Runtime (Germline FASTQ to VCF; human WGS at 40x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCPU-equivalent GATK germline pipeline on a CPU node, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 40x, column 'CPU' |
|---|
| Configuration: CPU-equivalent GATK germline pipeline on a CPU node (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 30h Runtime (Germline FASTQ to VCF; human WGS at 50x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCPU-equivalent GATK germline pipeline on a CPU node, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 50x, column 'CPU' |
|---|
| Configuration: CPU-equivalent GATK germline pipeline on a CPU node (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 35h Runtime (Germline FASTQ to VCF; human WGS at 60x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCPU-equivalent GATK germline pipeline on a CPU node, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 60x, column 'CPU' |
|---|
| Configuration: Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 A100 GPUs (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 2h 30m Runtime (Germline FASTQ to VCF; human WGS at 100x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceParabricks germline v4.3.0 (GeNePi PB_germ) on 2 A100 GPUs, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 100x, column 'GPU-2xA100' |
|---|
| Configuration: Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 A100 GPUs (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 42 m Runtime (Germline FASTQ to VCF; human WGS at 30x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceParabricks germline v4.3.0 (GeNePi PB_germ) on 2 A100 GPUs, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 30x, column 'GPU-2xA100' |
|---|
| Configuration: Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 A100 GPUs (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 1h 06m Runtime (Germline FASTQ to VCF; human WGS at 40x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceParabricks germline v4.3.0 (GeNePi PB_germ) on 2 A100 GPUs, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 40x, column 'GPU-2xA100' |
|---|
| Configuration: Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 A100 GPUs (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 1h 12m Runtime (Germline FASTQ to VCF; human WGS at 50x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceParabricks germline v4.3.0 (GeNePi PB_germ) on 2 A100 GPUs, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 50x, column 'GPU-2xA100' |
|---|
| Configuration: Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 A100 GPUs (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 1h 24m Runtime (Germline FASTQ to VCF; human WGS at 60x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceParabricks germline v4.3.0 (GeNePi PB_germ) on 2 A100 GPUs, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 60x, column 'GPU-2xA100' |
|---|
| Configuration: Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 V100 GPUs (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 6h 30m Runtime (Germline FASTQ to VCF; human WGS at 100x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceParabricks germline v4.3.0 (GeNePi PB_germ) on 2 V100 GPUs, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 100x, column 'GPU-2xV100' |
|---|
| Configuration: Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 V100 GPUs (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 1h 36m Runtime (Germline FASTQ to VCF; human WGS at 30x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceParabricks germline v4.3.0 (GeNePi PB_germ) on 2 V100 GPUs, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 30x, column 'GPU-2xV100' |
|---|
| Configuration: Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 V100 GPUs (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 2h 06m Runtime (Germline FASTQ to VCF; human WGS at 40x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceParabricks germline v4.3.0 (GeNePi PB_germ) on 2 V100 GPUs, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 40x, column 'GPU-2xV100' |
|---|
| Configuration: Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 V100 GPUs (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 2h 24m Runtime (Germline FASTQ to VCF; human WGS at 50x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceParabricks germline v4.3.0 (GeNePi PB_germ) on 2 V100 GPUs, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 50x, column 'GPU-2xV100' |
|---|
| Configuration: Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 V100 GPUs (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 3h 42m Runtime (Germline FASTQ to VCF; human WGS at 60x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceParabricks germline v4.3.0 (GeNePi PB_germ) on 2 V100 GPUs, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 60x, column 'GPU-2xV100' |
|---|
| Configuration: Parabricks germline v4.3.0 (GeNePi PB_germ) on 4 A100 GPUs (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 2h 06m Runtime (Germline FASTQ to VCF; human WGS at 100x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceParabricks germline v4.3.0 (GeNePi PB_germ) on 4 A100 GPUs, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 100x, column 'GPU-4xA100' |
|---|
| Configuration: Parabricks germline v4.3.0 (GeNePi PB_germ) on 4 A100 GPUs (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 30m Runtime (Germline FASTQ to VCF; human WGS at 30x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceParabricks germline v4.3.0 (GeNePi PB_germ) on 4 A100 GPUs, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 30x, column 'GPU-4xA100' |
|---|
| Configuration: Parabricks germline v4.3.0 (GeNePi PB_germ) on 4 A100 GPUs (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 42m Runtime (Germline FASTQ to VCF; human WGS at 40x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceParabricks germline v4.3.0 (GeNePi PB_germ) on 4 A100 GPUs, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 40x, column 'GPU-4xA100' |
|---|
| Configuration: Parabricks germline v4.3.0 (GeNePi PB_germ) on 4 A100 GPUs (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 1h 00m Runtime (Germline FASTQ to VCF; human WGS at 50x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceParabricks germline v4.3.0 (GeNePi PB_germ) on 4 A100 GPUs, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 50x, column 'GPU-4xA100' |
|---|
| Configuration: Parabricks germline v4.3.0 (GeNePi PB_germ) on 4 A100 GPUs (Marangoni et al. 2026) | Protocol: Germline FASTQ-to-VCF runtime by read depth, Parabricks v4.3.0 on V100 and A100 GPUs versus the CPU GATK equivalent (Marangoni et al. 2026 Table S1)
Dataset: Human WGS paired-end data at 30x, 40x, 50x, 60x and 100x average depth (Marangoni et al. 2026 Table S1) | 1h 12m Runtime (Germline FASTQ to VCF; human WGS at 60x average depth) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceParabricks germline v4.3.0 (GeNePi PB_germ) on 4 A100 GPUs, runtime by depth (Marangoni et al. 2026) model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth Aggregation: Not reported GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis; GeNePi: Supplementary Information · Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 60x, column 'GPU-4xA100' |
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