rewirebio.iobenchmarks
Protocol

WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)

Elapsed runtime and cost per sample for two ultra-rapid germline pipelines on cost-matched GCP VMs, WGS samples.

2 evaluations · 18 results

Overview

Elapsed runtime and cost per sample for two ultra-rapid germline pipelines on cost-matched GCP VMs, WGS samples.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

2 recorded evaluations, 18 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

2 evaluations · 18 results. Different protocols are not a single leaderboard.

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: NVIDIA Parabricks Germline v4.0.1-1 on a GCP VM with 48 vCPUs, 58 GB memory and 1 T4 GPU (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
9.43 compute-cost
us-dollar · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Parabricks on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), D14; ID 'ERR1955532'; Software 'Parabricks'; column 'Cost ($)'
Configuration: NVIDIA Parabricks Germline v4.0.1-1 on a GCP VM with 48 vCPUs, 58 GB memory and 1 T4 GPU (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
4:20:00 runtime
second · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Parabricks on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), C14; ID 'ERR1955532'; Software 'Parabricks'; column 'Runtime (h/m/s)'
Configuration: NVIDIA Parabricks Germline v4.0.1-1 on a GCP VM with 48 vCPUs, 58 GB memory and 1 T4 GPU (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
8.16 compute-cost
us-dollar · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Parabricks on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), D16; ID 'ERR1955536'; Software 'Parabricks'; column 'Cost ($)'
Configuration: NVIDIA Parabricks Germline v4.0.1-1 on a GCP VM with 48 vCPUs, 58 GB memory and 1 T4 GPU (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
4:22:00 runtime
second · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Parabricks on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), C16; ID 'ERR1955536'; Software 'Parabricks'; column 'Runtime (h/m/s)'
Configuration: NVIDIA Parabricks Germline v4.0.1-1 on a GCP VM with 48 vCPUs, 58 GB memory and 1 T4 GPU (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
10.6 compute-cost
us-dollar · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Parabricks on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), D18; ID 'ERR1955539'; Software 'Parabricks'; column 'Cost ($)'
Configuration: NVIDIA Parabricks Germline v4.0.1-1 on a GCP VM with 48 vCPUs, 58 GB memory and 1 T4 GPU (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
8.13 compute-cost
us-dollar · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Parabricks on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), D20; ID 'ERR1955540'; Software 'Parabricks'; column 'Cost ($)'
Configuration: NVIDIA Parabricks Germline v4.0.1-1 on a GCP VM with 48 vCPUs, 58 GB memory and 1 T4 GPU (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
4:06:00 runtime
second · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Parabricks on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), C20; ID 'ERR1955540'; Software 'Parabricks'; column 'Runtime (h/m/s)'
Configuration: NVIDIA Parabricks Germline v4.0.1-1 on a GCP VM with 48 vCPUs, 58 GB memory and 1 T4 GPU (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
10.6 compute-cost
us-dollar · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Parabricks on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), D22; ID 'ERR1955541'; Software 'Parabricks'; column 'Cost ($)'
Configuration: NVIDIA Parabricks Germline v4.0.1-1 on a GCP VM with 48 vCPUs, 58 GB memory and 1 T4 GPU (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
4:40:00 runtime
second · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Parabricks on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), C22; ID 'ERR1955541'; Software 'Parabricks'; column 'Runtime (h/m/s)'
Configuration: Sentieon DNASeq v202308 on a GCP VM with 64 vCPUs and 57 GB memory (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
10 compute-cost
us-dollar · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Sentieon on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), D13; ID 'ERR1955532'; Software 'Sentieon'; column 'Cost ($)'
Configuration: Sentieon DNASeq v202308 on a GCP VM with 64 vCPUs and 57 GB memory (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
10.7 compute-cost
us-dollar · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Sentieon on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), D15; ID 'ERR1955536'; Software 'Sentieon'; column 'Cost ($)'
Configuration: Sentieon DNASeq v202308 on a GCP VM with 64 vCPUs and 57 GB memory (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
3:00:00 runtime
second · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Sentieon on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), C15; ID 'ERR1955536'; Software 'Sentieon'; column 'Runtime (h/m/s)'
Configuration: Sentieon DNASeq v202308 on a GCP VM with 64 vCPUs and 57 GB memory (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
9.76 compute-cost
us-dollar · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Sentieon on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), D17; ID 'ERR1955539'; Software 'Sentieon'; column 'Cost ($)'
Configuration: Sentieon DNASeq v202308 on a GCP VM with 64 vCPUs and 57 GB memory (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
3:45:00 runtime
second · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Sentieon on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), C17; ID 'ERR1955539'; Software 'Sentieon'; column 'Runtime (h/m/s)'
Configuration: Sentieon DNASeq v202308 on a GCP VM with 64 vCPUs and 57 GB memory (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
8.02 compute-cost
us-dollar · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Sentieon on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), D19; ID 'ERR1955540'; Software 'Sentieon'; column 'Cost ($)'
Configuration: Sentieon DNASeq v202308 on a GCP VM with 64 vCPUs and 57 GB memory (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
3:02:00 runtime
second · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Sentieon on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), C19; ID 'ERR1955540'; Software 'Sentieon'; column 'Runtime (h/m/s)'
Configuration: Sentieon DNASeq v202308 on a GCP VM with 64 vCPUs and 57 GB memory (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
9.44 compute-cost
us-dollar · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Sentieon on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), D21; ID 'ERR1955541'; Software 'Sentieon'; column 'Cost ($)'
Configuration: Sentieon DNASeq v202308 on a GCP VM with 64 vCPUs and 57 GB memory (Franzoso et al. 2025)Protocol: WGS FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
Dataset: Five WGS samples from Illumina's Polaris project (HiSeq X, 150 bp reads)
3:50:00 runtime
second · lower

Uncertainty: Not reported by the source: Single run per cell

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Sentieon on GCP, WGS samples (Franzoso et al. 2025)

model-execution-20261009-protocol-franzoso2025-wgs-gcp

Aggregation: Not reported

Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), C21; ID 'ERR1955541'; Software 'Sentieon'; column 'Runtime (h/m/s)'

Source checking is not independent reproduction. Release 2026-10-09-8cc1db47c7f9.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

External evaluations
2

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Select a task-valid null control after reviewing inputs and metric

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Select an upstream conventional reference after reviewing the full protocol

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-09-8cc1db47c7f9. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

Evidence

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Evidence table

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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.

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Claims, original sources and review scope · Release 2026-10-09-8cc1db47c7f9
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Sources and history

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

2 source records and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: model-execution-20261009-protocol-franzoso2025-wgs-gcp

areas
dna-genomes
contexts
clinical_research
protocol
Each pipeline run from raw FASTQ to VCF with default parameters on its own GCP VM; start and end times and cost from GCP monitoring (Ops Agent).
version
Table S2 rows for the WGS samples
metric
runtime
denominator
5
limitations
One run per sample and pipeline; no repeats.; The two VMs were chosen for similar hourly cost (1.79 and 1.65 USD), not similar hardware. The text says Parabricks used the available 16 CPUs on genomes, but Methods give the Parabricks VM 48 vCPUs.; Costs exclude the Sentieon licence fee (Discussion paragraph 10).; Accuracy of the calls is not reported.; Two WGS runtime cells (Table S2 C13, ERR1955532 Sentieon 0:03:21; C18, ERR1955539 Parabricks 0:04:41) cannot be WGS runtimes and disagree with the ranges in Results; both results are disputed and not shown. They look entered as hours and minutes, but the source does not confirm it.
missing metadata
metric implementation: reason: unreported; note: How cost per sample was computed from the GCP billing is not stated
source locator
Table S2; Methods 'Data Collection and Analysis'
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