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)

Execution time of the GeNePi PB_germ module and its CPU equivalent at five depths.

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4 recorded evaluations, 20 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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4 evaluations · 20 results. Different protocols are not a single leaderboard.

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)

Sorted by Runtime (Germline FASTQ to VCF; human WGS at 100x average depth) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Runtime (Germline FASTQ to VCF; human WGS at 100x average depth)	Runtime (Germline FASTQ to VCF; human WGS at 30x average depth)	Runtime (Germline FASTQ to VCF; human WGS at 40x average depth)	Runtime (Germline FASTQ to VCF; human WGS at 50x average depth)	Runtime (Germline FASTQ to VCF; human WGS at 60x average depth)
Parabricks germline v4.3.0 (GeNePi PB_germ) on 4 A100 GPUs (Marangoni et al. 2026)Evaluation	2h 06m (best in column)	30m (best in column)	42m (best in column)	1h 00m (best in column)	1h 12m (best in column)
Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 A100 GPUs (Marangoni et al. 2026)Evaluation	2h 30m	42 m	1h 06m	1h 12m	1h 24m
Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 V100 GPUs (Marangoni et al. 2026)Evaluation	6h 30m	1h 36m	2h 06m	2h 24m	3h 42m
CPU-equivalent GATK germline pipeline on a CPU node (Marangoni et al. 2026)Evaluation	60h	17h	24h	30h	35h

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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

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Technical metadata and extraction receipts

Stable ID: model-execution-20261011-protocol-marangoni2026-germline-runtime-by-depth

areas: dna-genomes
contexts: clinical_research
protocol: Parabricks germline pipeline v4.3.0 (alignment to GRCh38 through HaplotypeCaller) in the GeNePi PB_germ module, and the CPU-equivalent BWA-MEM plus GATK pipeline, run on HPC nodes; execution time per run.
version: Supplementary Table S1
metric: runtime
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.
source locator: Supplementary S3.1-S3.2; Table S1

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