23.8 runtime
samarakoon2025-dragen42-server-v2-hc runtime (HaplotypeCaller or DRAGEN GSVC calling stage; sample NA12889 (52.80x))
- Tested configuration
- Illumina DRAGEN v4.2 on DRAGEN server V2 (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
- Procedure
- model-execution-20261009-protocol-samarakoon2025-hc
- Evaluation
- Illumina DRAGEN v4.2 on DRAGEN server V2, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source: Single recorded run per cell; no repeats or intervals printed
- Evidence
- Independent external evaluation · source checkedBenchmarking 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 'DRAGEN' (PDF page text)
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
- Ten WGS samples
- Adaptation
- Not reported
- Scoring implementation
- Wall-clock time per stage (Methods 2.6)
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 23.75 Individual claims | Benchmarking accelerated next-generation sequencing analysis pipelines Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12889', column 'DRAGEN' (PDF page text) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics Advances 5(1):vbaf085, published 2025-05-15; PMC12092081 full-text XML | source checked ["source-hash-verification","pdf-text-parse","independent-cell-check"] · 2026-10-09T20:46:48Z independent paper Audit detailsExtracted by deterministic parse of the pinned supplementary PDF text layer (pdftotext version 26.08.0, -layout) in extract/extract_model_execution.py, with table titles, sub-table headings, column headers and sample labels asserted. printed_value is the number as printed. Independent review 2026-10-09: printed value, numeric value, metric, qualifier, unit, direction, locator and configuration and protocol identity match the source. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
| Reported result 23.75 Individual claims | 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 'DRAGEN' (PDF page text) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 'Publication-ready_Supplementary materials-20250404.pdf' inside vbaf085_supplementary_data.zip | source checked ["source-hash-verification","pdf-text-parse","independent-cell-check"] · 2026-10-09T20:46:48Z independent paper Audit detailsExtracted by deterministic parse of the pinned supplementary PDF text layer (pdftotext version 26.08.0, -layout) in extract/extract_model_execution.py, with table titles, sub-table headings, column headers and sample labels asserted. printed_value is the number as printed. Independent review 2026-10-09: printed value, numeric value, metric, qualifier, unit, direction, locator and configuration and protocol identity match the source. Field: Source artifact SHA-256: Hash scope: SHA-256 of the PDF. The publisher zip vbaf085_supplementary_data.zip that contains it has SHA-256 a828608e459ec1fe57828e9b4fbce228e9507b8686eecedac323f45fd4c3cc07. Retrieved inside the Europe PMC supplementaryFiles zip, which is assembled per request; the publisher's inner zip and the PDF it holds are pinned. Archive member: Publication-ready_Supplementary materials-20250404.pdf Extraction artifact SHA-256: |
Sources and history
Release 2026-10-09-8cc1db47c7f9 · Record review: source checked
2 source records and release history
- 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
Technical metadata and extraction receipts
Stable ID: model-execution-20261009-result-samarakoon2025-dragen42-server-v2-hc-na12889
- metric
- runtime
- metric direction
- lower
- unit
- minute
- metric qualifier
- HaplotypeCaller or DRAGEN GSVC calling stage; sample NA12889 (52.80x)
- printed value
- 23.75
- numeric value
- 23.75
- source locator
- Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12889', column 'DRAGEN' (PDF page text)
- missing metadata
- uncertainty: reason: unreported; note: Single recorded run per cell; no repeats or intervals printed
- review
- method: source-hash-verification; pdf-text-parse; independent-cell-check; method note: Re-downloaded the Europe PMC supplementaryFiles zip, unpacked the publisher zip and matched the PDF's SHA-256. Converted the PDF with pdftotext -layout and parsed Tables S1, S3 and S4 with a separate script written for this review (the extractor's scripts were not imported or run), asserting sub-table headings, the column header and ten sample labels per sub-table. Checked printed and numeric value, metric, qualifier (sample and coverage against Table S1), unit, direction, locator, and the linked evaluation's configuration and protocol. Recomputed every Table S3c total from its read-mapping and HC or GSVC stage values.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; reviewed at: 2026-10-09T20:46:48Z; artifact sha256: 5fbee07d1a14336e909daf2c6fdd3b26af4c252fae135c033a84c596b2a5d7db; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12092081/supplementaryFiles; note: Extracted by deterministic parse of the pinned supplementary PDF text layer (pdftotext version 26.08.0, -layout) in extract/extract_model_execution.py, with table titles, sub-table headings, column headers and sample labels asserted. printed_value is the number as printed. Independent review 2026-10-09: printed value, numeric value, metric, qualifier, unit, direction, locator and configuration and protocol identity match the source.