Relevance of Germline runtime by read depth, Parabricks on V100 and A100 versus CPU GATK (Marangoni et al. 2026) to "Select an execution workflow for large-scale diagnostic genomics"
- Use case
- Select an execution workflow for large-scale diagnostic genomics
- Assessed by
- 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)
- Relevance
- Direct evidence
- Endpoint
- FASTQ-to-VCF germline runtime of Parabricks v4.3.0 on 2 V100, 2 A100 and 4 A100 GPU nodes and of the CPU GATK equivalent at 30x, 40x, 50x, 60x and 100x WGS
Directly measures how per-genome germline runtime scales with read depth for CPU and three GPU set-ups on stated HPC hardware, built by a regional genomics centre for routine WGS, which matches the resource and throughput part of the question. Limits: one unnamed sample per depth, an unstated number of runs per value and author-reported GPU rows.
4 reviewed evaluations
- CPU-equivalent GATK germline pipeline on a CPU node, runtime by depth (Marangoni et al. 2026)
- Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 A100 GPUs, runtime by depth (Marangoni et al. 2026)
- Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 V100 GPUs, runtime by depth (Marangoni et al. 2026)
- Parabricks germline v4.3.0 (GeNePi PB_germ) on 4 A100 GPUs, runtime by depth (Marangoni et al. 2026)
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
36 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Citation locations2 values
| GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis model-execution-20261011-source-marangoni2026-genepi-supplement: Supplementary S3.1-S3.2; Table S1; model-execution-20261011-source-marangoni2026-genepi: Results 'Benchmarking'; Figure 2; Competing interest Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 27(1), published 2026-01-25; PMC12832024 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Citation locations2 values
| GeNePi: Supplementary Information model-execution-20261011-source-marangoni2026-genepi-supplement: Supplementary S3.1-S3.2; Table S1; model-execution-20261011-source-marangoni2026-genepi: Results 'Benchmarking'; Figure 2; Competing interest Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: genepi_supplinfo_rev_bbag001.pdf from the Europe PMC supplementary files of PMC12832024 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: genepi_supplinfo_rev_bbag001.pdf |
| Comparison group marangoni2026-depth Context-only references | GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis model-execution-20261011-source-marangoni2026-genepi-supplement: Supplementary S3.1-S3.2; Table S1; model-execution-20261011-source-marangoni2026-genepi: Results 'Benchmarking'; Figure 2; Competing interest Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 27(1), published 2026-01-25; PMC12832024 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison group marangoni2026-depth Context-only references | GeNePi: Supplementary Information model-execution-20261011-source-marangoni2026-genepi-supplement: Supplementary S3.1-S3.2; Table S1; model-execution-20261011-source-marangoni2026-genepi: Results 'Benchmarking'; Figure 2; Competing interest Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: genepi_supplinfo_rev_bbag001.pdf from the Europe PMC supplementary files of PMC12832024 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: genepi_supplinfo_rev_bbag001.pdf |
| Comparison title Parabricks on V100 and A100 versus CPU GATK by read depth (Marangoni et al. 2026) Context-only references | GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis model-execution-20261011-source-marangoni2026-genepi-supplement: Supplementary S3.1-S3.2; Table S1; model-execution-20261011-source-marangoni2026-genepi: Results 'Benchmarking'; Figure 2; Competing interest Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 27(1), published 2026-01-25; PMC12832024 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison title Parabricks on V100 and A100 versus CPU GATK by read depth (Marangoni et al. 2026) Context-only references | GeNePi: Supplementary Information model-execution-20261011-source-marangoni2026-genepi-supplement: Supplementary S3.1-S3.2; Table S1; model-execution-20261011-source-marangoni2026-genepi: Results 'Benchmarking'; Figure 2; Competing interest Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: genepi_supplinfo_rev_bbag001.pdf from the Europe PMC supplementary files of PMC12832024 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: genepi_supplinfo_rev_bbag001.pdf |
Constraints2 values
| GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis model-execution-20261011-source-marangoni2026-genepi-supplement: Supplementary S3.1-S3.2; Table S1; model-execution-20261011-source-marangoni2026-genepi: Results 'Benchmarking'; Figure 2; Competing interest Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 27(1), published 2026-01-25; PMC12832024 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints2 values
| GeNePi: Supplementary Information model-execution-20261011-source-marangoni2026-genepi-supplement: Supplementary S3.1-S3.2; Table S1; model-execution-20261011-source-marangoni2026-genepi: Results 'Benchmarking'; Figure 2; Competing interest Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: genepi_supplinfo_rev_bbag001.pdf from the Europe PMC supplementary files of PMC12832024 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: genepi_supplinfo_rev_bbag001.pdf |
| Endpoint FASTQ-to-VCF germline runtime of Parabricks v4.3.0 on 2 V100, 2 A100 and 4 A100 GPU nodes and of the CPU GATK equivalent at 30x, 40x, 50x, 60x and 100x WGS Context-only references | GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis model-execution-20261011-source-marangoni2026-genepi-supplement: Supplementary S3.1-S3.2; Table S1; model-execution-20261011-source-marangoni2026-genepi: Results 'Benchmarking'; Figure 2; Competing interest Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 27(1), published 2026-01-25; PMC12832024 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Endpoint FASTQ-to-VCF germline runtime of Parabricks v4.3.0 on 2 V100, 2 A100 and 4 A100 GPU nodes and of the CPU GATK equivalent at 30x, 40x, 50x, 60x and 100x WGS Context-only references | GeNePi: Supplementary Information model-execution-20261011-source-marangoni2026-genepi-supplement: Supplementary S3.1-S3.2; Table S1; model-execution-20261011-source-marangoni2026-genepi: Results 'Benchmarking'; Figure 2; Competing interest Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: genepi_supplinfo_rev_bbag001.pdf from the Europe PMC supplementary files of PMC12832024 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: genepi_supplinfo_rev_bbag001.pdf |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis · Original source · Briefings in Bioinformatics 27(1), published 2026-01-25; PMC12832024 full-text XML
- GeNePi: Supplementary Information · Original source · genepi_supplinfo_rev_bbag001.pdf from the Europe PMC supplementary files of PMC12832024
Technical metadata and extraction receipts
Stable ID: use-case-mapping-model-execution-20261011-marangoni2026-germline-runtime-by-depth
- field
- links:assessed_by:model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth
- value
- model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth
- relevance
- direct
- endpoint
- FASTQ-to-VCF germline runtime of Parabricks v4.3.0 on 2 V100, 2 A100 and 4 A100 GPU nodes and of the CPU GATK equivalent at 30x, 40x, 50x, 60x and 100x WGS
- rationale
- Directly measures how per-genome germline runtime scales with read depth for CPU and three GPU set-ups on stated HPC hardware, built by a regional genomics centre for routine WGS, which matches the resource and throughput part of the question. Limits: one unnamed sample per depth, an unstated number of runs per value and author-reported GPU rows.
- constraints
- Inspect every linked evaluation's source locator before citing a result.; Do not combine this mapping's evaluations with any other protocol's results; hardware, inputs, software versions and timing boundaries differ between sources.
- limitations
- Author-reported for the GPU rows: the authors built GeNePi, whose PB_germ module wraps Parabricks; no competing interests declared.; The input sample is not named for Table S1; the depths (30x to 100x) are average read depths of human WGS data.; One value per depth and hardware configuration is printed; the number of runs behind it is not stated and no spread is printed.; Hardware differs between columns (different CPUs, RAM and GPU counts), so differences mix software and hardware.; CPU runtimes are printed in whole hours.; Accuracy of the calls is reported separately (synthetic and HG002 data), not beside runtime.; Several numbers in the article's running text are missing from the XML (rendered as blank formulae), so the text cannot be checked against Table S1.; The article states a 10- to 78-fold average acceleration over CPU (Discussion, citing Figure 2 and Supplementary Figure S11); the Table S1 ratios run from about 10 to 34, so the upper figure comes from runs not in Table S1.
- revision
- 1
- reason
- Add primary-source execution evidence from the diagnostic genomics execution literature pass (2026-10-11).
- citation locators
- source id: model-execution-20261011-source-marangoni2026-genepi-supplement; locator: Supplementary S3.1-S3.2; Table S1; source id: model-execution-20261011-source-marangoni2026-genepi; locator: Results 'Benchmarking'; Figure 2; Competing interest
- source locator
- model-execution-20261011-source-marangoni2026-genepi-supplement: Supplementary S3.1-S3.2; Table S1; model-execution-20261011-source-marangoni2026-genepi: Results 'Benchmarking'; Figure 2; Competing interest
- comparison group
- marangoni2026-depth
- comparison title
- Parabricks on V100 and A100 versus CPU GATK by read depth (Marangoni et al. 2026)
- headline metric
- runtime
- review
- method: source-hash-verification; independent-cell-check; scope-review; reviewer: claude; reviewer note: Claude (Opus 5.5) research agent uc-execution extracted and drafted; Claude (Opus 5.5) review agent reviewer-exec checked every value and this judgement against the pinned sources; reviewed at: 2026-10-12T07:50:32Z; note: Bounded primary-source transcription with independent cell check and relevance review. No execution, reproduction, qualified human scientific review or clinical validation.
- reviewed evaluations
- model-execution-20261011-eval-marangoni2026-gatk-cpu; model-execution-20261011-eval-marangoni2026-parabricks-4-3-0-2xa100; model-execution-20261011-eval-marangoni2026-parabricks-4-3-0-2xv100; model-execution-20261011-eval-marangoni2026-parabricks-4-3-0-4xa100
- pins
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