Parabricks germline v4.3.0 (GeNePi PB_germ) on 2 V100 GPUs (Marangoni et al. 2026)
GeNePi PB_germ module: Parabricks germline pipeline v4.3.0 (alignment to GRCh38, duplicate marking, BQSR, HaplotypeCaller)
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Evaluations and results
1 evaluation · 5 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 2 V100 GPUs (Marangoni et al. 2026)Evaluation | 6h 30m | 1h 36m | 2h 06m | 2h 24m | 3h 42m |
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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-config-marangoni2026-parabricks-4-3-0-2xv100
- areas
- dna-genomes
- contexts
- clinical_research
- method types
- conventional_pipeline
- reported name
- GPU-2xV100
- foundation model eligible
- false
- hardware
- description: Two Xeon 6244 CPUs, 384 GB RAM, two NVIDIA Tesla V100-PCIE-32GB (Supplementary S3.1)
- protocol
- GeNePi PB_germ module: Parabricks germline pipeline v4.3.0 (alignment to GRCh38, duplicate marking, BQSR, HaplotypeCaller)
- access reuse
- GeNePi is open source; Parabricks is NVIDIA software
- source locator
- Supplementary S3.1-S3.2; Table S1 column 'GPU-2xV100'
- version
- v4.3.0