Runtime (Germline FASTQ to VCF; human WGS at 40x average depth) of Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 V100 GPUs (Marangoni et al. 2026) on 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)
Methods
- Tested 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)
- Procedure
- 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)
- Evaluation
- Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 V100 GPUs, runtime by depth (Marangoni et al. 2026)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Author-reported evaluation · source checkedGeNePi: 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'
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- Five average depths, one value each; number of runs not stated
- Adaptation
- Not reported
- Scoring implementation
- Not reported
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
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.
2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 2h 06m Individual claims | GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 40x, column 'GPU-2xV100' 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 | source checked ["source-hash-verification","pdf-text-parse","rendered-source-visual-check","independent-cell-check"] · 2026-10-12T07:50:32Z author reported Audit detailsIndependent review 2026-10-12: printed value, numeric value, metric, qualifier, unit, direction, uncertainty, locator and configuration and protocol identity match the source. Transcribed, not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
| Reported result 2h 06m Individual claims | GeNePi: Supplementary Information Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 40x, column 'GPU-2xV100' 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 | source checked ["source-hash-verification","pdf-text-parse","rendered-source-visual-check","independent-cell-check"] · 2026-10-12T07:50:32Z author reported Audit detailsIndependent review 2026-10-12: printed value, numeric value, metric, qualifier, unit, direction, uncertainty, locator and configuration and protocol identity match the source. Transcribed, not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: genepi_supplinfo_rev_bbag001.pdf Extraction artifact SHA-256: |
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: model-execution-20261011-result-marangoni2026-parabricks-4-3-0-2xv100-40x-runtime
- metric
- runtime
- metric direction
- lower
- unit
- minute
- metric qualifier
- Germline FASTQ to VCF; human WGS at 40x average depth
- unit detail
- printed as hours and minutes; numeric_value in minutes
- printed value
- 2h 06m
- numeric value
- 126
- source locator
- Supplementary Table S1 (page 7), row 'Avg. Reads Depth' 40x, column 'GPU-2xV100'
- missing metadata
- uncertainty: reason: unreported
- review
- method: source-hash-verification; pdf-text-parse; rendered-source-visual-check; independent-cell-check; method note: Re-downloaded the Europe PMC supplementaryFiles zip and matched the PDF member's SHA-256; article XML re-downloaded and matched. Table S1 parsed from pdftotext -layout with a separate review script, minutes recomputed from the printed hours and minutes, and every cell read against a 150 dpi render of page 7.; reviewer: claude; reviewer note: Claude (Opus 5.5) review agent reviewer-exec, independent of the extractor uc-execution; no human review claimed; reviewed at: 2026-10-12T07:50:32Z; artifact sha256: afa166a30320efd633cb28ddc91a05082854b0ef5e6593333c0ce9dbd2ae1bb9; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12832024/supplementaryFiles; note: Independent review 2026-10-12: printed value, numeric value, metric, qualifier, unit, direction, uncertainty, locator and configuration and protocol identity match the source. Transcribed, not reproduced.