Configuration

CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)

CPU column of Supplementary Table S3.

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CPU column of Supplementary Table S3.

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Release 2026-10-09-8cc1db47c7f9 · Record review: source checked

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Benchmarking accelerated next-generation sequencing analysis pipelines · Original source · Bioinformatics Advances 5(1):vbaf085, published 2025-05-15; PMC12092081 full-text XML
Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Original source · 'Publication-ready_Supplementary materials-20250404.pdf' inside vbaf085_supplementary_data.zip

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Technical metadata and extraction receipts

Stable ID: model-execution-20261009-config-samarakoon2025-cpu-epyc7702

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
foundation model eligible: false
reported name: CPU
protocol: BWA, SAMtools and GATK release 4.0.3.0 (MarkDuplicates, BaseRecalibrator, ApplyBQSR, HaplotypeCaller) or DeepVariant; parameters from nf-core/sarek
hardware: description: AMD EPYC 7702 (64 cores), 128-256 GB RAM, GPFS storage, Fox HPC cluster at the University of Oslo, nodes not exclusive
source locator: Supplementary Table S2; Methods 2.2-2.5; Table S3 column header
version: GATK release 4.0.3.0
missing metadata: packages: reason: unreported; note: BWA, SAMtools and DeepVariant versions are not stated

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, DeepVariant calling stage (Samarakoon et al. 2025 Table S3b.2) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	338 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), DeepVariant calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-dv Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.2). Variant calling via DV', row 'NA12778', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, DeepVariant calling stage (Samarakoon et al. 2025 Table S3b.2) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	252 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), DeepVariant calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-dv Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.2). Variant calling via DV', row 'NA12812', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, DeepVariant calling stage (Samarakoon et al. 2025 Table S3b.2) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	313 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), DeepVariant calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-dv Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.2). Variant calling via DV', row 'NA12829', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, DeepVariant calling stage (Samarakoon et al. 2025 Table S3b.2) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	291 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), DeepVariant calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-dv Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.2). Variant calling via DV', row 'NA12843', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, DeepVariant calling stage (Samarakoon et al. 2025 Table S3b.2) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	429 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), DeepVariant calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-dv Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.2). Variant calling via DV', row 'NA12877', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, DeepVariant calling stage (Samarakoon et al. 2025 Table S3b.2) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	435 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), DeepVariant calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-dv Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.2). Variant calling via DV', row 'NA12878', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, DeepVariant calling stage (Samarakoon et al. 2025 Table S3b.2) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	488 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), DeepVariant calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-dv Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.2). Variant calling via DV', row 'NA12889', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, DeepVariant calling stage (Samarakoon et al. 2025 Table S3b.2) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	428 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), DeepVariant calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-dv Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.2). Variant calling via DV', row 'NA12890', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, DeepVariant calling stage (Samarakoon et al. 2025 Table S3b.2) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	465 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), DeepVariant calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-dv Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.2). Variant calling via DV', row 'NA12891', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, DeepVariant calling stage (Samarakoon et al. 2025 Table S3b.2) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	465 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), DeepVariant calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-dv Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.2). Variant calling via DV', row 'NA12892', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	614 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12778', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	557 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12812', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	756 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12829', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	603 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12843', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	1150 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12877', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	1110 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12878', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	1350 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12889', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	1290 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12890', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	1090 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12891', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	1150 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12892', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, read mapping stage (Samarakoon et al. 2025 Table S3a) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	334 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), read mapping stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-mapping Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'a) Read mapping', row 'NA12778', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, read mapping stage (Samarakoon et al. 2025 Table S3a) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	267 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), read mapping stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-mapping Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'a) Read mapping', row 'NA12812', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, read mapping stage (Samarakoon et al. 2025 Table S3a) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	508 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), read mapping stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-mapping Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'a) Read mapping', row 'NA12829', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, read mapping stage (Samarakoon et al. 2025 Table S3a) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	354 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), read mapping stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-mapping Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'a) Read mapping', row 'NA12843', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, read mapping stage (Samarakoon et al. 2025 Table S3a) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	1270 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), read mapping stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-mapping Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'a) Read mapping', row 'NA12877', column 'CPU' (PDF page text)