Evaluation

Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification: genus level, read-count cut-off 0 (Carbo et al. 2022)

Published RNA metagenomic pathogen-detection comparison; transcribed, not reproduced.

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Evaluation results

1 evaluation · 11 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022)	Protocol: Respiratory virus detection against PCR, genus level, read-count cut-off 0 (Carbo et al. 2022 Supplementary Table 1) Dataset: Nasal washings from COPD patients with respiratory complaints, metagenomic sequencing and 13-target respiratory PCR panel (Carbo et al. 2022)	0.948 auroc unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification: genus level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-genus-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', cell D18, row 'GD', column 'AUC'
Configuration: Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022)	Protocol: Respiratory virus detection against PCR, genus level, read-count cut-off 0 (Carbo et al. 2022 Supplementary Table 1) Dataset: Nasal washings from COPD patients with respiratory complaints, metagenomic sequencing and 13-target respiratory PCR panel (Carbo et al. 2022)	38 regression-intercept unitless · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification: genus level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-genus-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', cell J18, row 'GD', column 'LR intercept'
Configuration: Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022)	Protocol: Respiratory virus detection against PCR, genus level, read-count cut-off 0 (Carbo et al. 2022 Supplementary Table 1) Dataset: Nasal washings from COPD patients with respiratory complaints, metagenomic sequencing and 13-target respiratory PCR panel (Carbo et al. 2022)	42.3% pearson-r-squared percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification: genus level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-genus-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', cell K18, row 'GD', column 'LR r2, %'
Configuration: Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022)	Protocol: Respiratory virus detection against PCR, genus level, read-count cut-off 0 (Carbo et al. 2022 Supplementary Table 1) Dataset: Nasal washings from COPD patients with respiratory complaints, metagenomic sequencing and 13-target respiratory PCR panel (Carbo et al. 2022)	-2.14 regression-slope unitless · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification: genus level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-genus-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', cell I18, row 'GD', column 'LR slope'
Configuration: Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022)	Protocol: Respiratory virus detection against PCR, genus level, read-count cut-off 0 (Carbo et al. 2022 Supplementary Table 1) Dataset: Nasal washings from COPD patients with respiratory complaints, metagenomic sequencing and 13-target respiratory PCR panel (Carbo et al. 2022)	0.997 negative-predictive-value fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification: genus level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-genus-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', cell H18, row 'GD', column 'NPV (ROC)'
Configuration: Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022)	Protocol: Respiratory virus detection against PCR, genus level, read-count cut-off 0 (Carbo et al. 2022 Supplementary Table 1) Dataset: Nasal washings from COPD patients with respiratory complaints, metagenomic sequencing and 13-target respiratory PCR panel (Carbo et al. 2022)	0.611 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification: genus level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-genus-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', cell G18, row 'GD', column 'PPV (ROC)'
Configuration: Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022)	Protocol: Respiratory virus detection against PCR, genus level, read-count cut-off 0 (Carbo et al. 2022 Supplementary Table 1) Dataset: Nasal washings from COPD patients with respiratory complaints, metagenomic sequencing and 13-target respiratory PCR panel (Carbo et al. 2022)	0.0853 roc-distance unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification: genus level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-genus-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', cell C18, row 'GD', column 'Informedness'
Configuration: Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022)	Protocol: Respiratory virus detection against PCR, genus level, read-count cut-off 0 (Carbo et al. 2022 Supplementary Table 1) Dataset: Nasal washings from COPD patients with respiratory complaints, metagenomic sequencing and 13-target respiratory PCR panel (Carbo et al. 2022)	0.917 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification: genus level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-genus-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', cell E18, row 'GD', column 'SN (ROC)'
Configuration: Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022)	Protocol: Respiratory virus detection against PCR, genus level, read-count cut-off 0 (Carbo et al. 2022 Supplementary Table 1) Dataset: Nasal washings from COPD patients with respiratory complaints, metagenomic sequencing and 13-target respiratory PCR panel (Carbo et al. 2022)	0.982 specificity fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification: genus level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-genus-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', cell F18, row 'GD', column 'SL (ROC)'
Configuration: Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022)	Protocol: Respiratory virus detection against PCR, genus level, read-count cut-off 0 (Carbo et al. 2022 Supplementary Table 1) Dataset: Nasal washings from COPD patients with respiratory complaints, metagenomic sequencing and 13-target respiratory PCR panel (Carbo et al. 2022)	10 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification: genus level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-genus-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', cell L18, row 'GD', column 'Taxa'
Configuration: Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022)	Protocol: Respiratory virus detection against PCR, genus level, read-count cut-off 0 (Carbo et al. 2022 Supplementary Table 1) Dataset: Nasal washings from COPD patients with respiratory complaints, metagenomic sequencing and 13-target respiratory PCR panel (Carbo et al. 2022)	10 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification: genus level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-genus-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', cell M18, row 'GD', column 'Taxa with reads >0'

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

Evaluation procedure

rna-pathogen-20261009-protocol-carbo2022-genus-cutoff-0

Configuration: Genome Detective, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022)
Protocol: Respiratory virus detection against PCR, genus level, read-count cut-off 0 (Carbo et al. 2022 Supplementary Table 1)
Dataset: Nasal washings from COPD patients with respiratory complaints, metagenomic sequencing and 13-target respiratory PCR panel (Carbo et al. 2022)

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-09
protocol id: rna-pathogen-20261009-protocol-carbo2022-genus-cutoff-0
dataset version: SRX6713943-SRX6714030
split: Whole cohort
population: 88 samples, 1144 PCR results (24 positive)
inputs: Trimmed NextSeq 150 bp paired-end reads
adaptation: Viral RefSeq database built 2020-12-27 (Genome Detective: own database)
metric implementation: Authors' ROC analysis over read-count cut-offs
aggregation: All PCR targets pooled
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Whole cohort
Adaptation: Viral RefSeq database built 2020-12-27 (Genome Detective: own database)
Scoring implementation: Authors' ROC analysis over read-count cut-offs

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

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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.

36 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-09-8cc1db47c7f9
Property and statement	Original source and location	Review and provenance
attributes.comparison.adaptation Viral RefSeq database built 2020-12-27 (Genome Detective: own database) Context-only references	Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort Original source ↗ Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', row 18; Row rank '#' as printed: 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Pathogens 11(3):340, published 2022-03-11; PMC8953373 full-text XML Retrieved: 2026-10-09T20:06:32Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `e6683855ad278a555598295fdc4166e54ddb0e39e3d971878b898b20bc8ddf95` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.adaptation Viral RefSeq database built 2020-12-27 (Genome Detective: own database) Context-only references	Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 Original source ↗ Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', row 18; Row rank '#' as printed: 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv 2022.01.21.22269647 version 1 (2022-01-21), supplementary file media-1.xlsx Retrieved: 2026-10-09T20:16:56Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `cd3a80d785b78377e79960d0280667f98cba3305d68426fdfaf8efeecd4542d7` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation All PCR targets pooled Context-only references	Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort Original source ↗ Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', row 18; Row rank '#' as printed: 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Pathogens 11(3):340, published 2022-03-11; PMC8953373 full-text XML Retrieved: 2026-10-09T20:06:32Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `e6683855ad278a555598295fdc4166e54ddb0e39e3d971878b898b20bc8ddf95` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation All PCR targets pooled Context-only references	Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 Original source ↗ Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', row 18; Row rank '#' as printed: 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv 2022.01.21.22269647 version 1 (2022-01-21), supplementary file media-1.xlsx Retrieved: 2026-10-09T20:16:56Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `cd3a80d785b78377e79960d0280667f98cba3305d68426fdfaf8efeecd4542d7` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget Not reported Context-only references	Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort Original source ↗ Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', row 18; Row rank '#' as printed: 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Pathogens 11(3):340, published 2022-03-11; PMC8953373 full-text XML Retrieved: 2026-10-09T20:06:32Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `e6683855ad278a555598295fdc4166e54ddb0e39e3d971878b898b20bc8ddf95` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget Not reported Context-only references	Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 Original source ↗ Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', row 18; Row rank '#' as printed: 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv 2022.01.21.22269647 version 1 (2022-01-21), supplementary file media-1.xlsx Retrieved: 2026-10-09T20:16:56Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `cd3a80d785b78377e79960d0280667f98cba3305d68426fdfaf8efeecd4542d7` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version SRX6713943-SRX6714030 Context-only references	Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort Original source ↗ Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', row 18; Row rank '#' as printed: 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Pathogens 11(3):340, published 2022-03-11; PMC8953373 full-text XML Retrieved: 2026-10-09T20:06:32Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `e6683855ad278a555598295fdc4166e54ddb0e39e3d971878b898b20bc8ddf95` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version SRX6713943-SRX6714030 Context-only references	Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 Original source ↗ Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', row 18; Row rank '#' as printed: 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv 2022.01.21.22269647 version 1 (2022-01-21), supplementary file media-1.xlsx Retrieved: 2026-10-09T20:16:56Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `cd3a80d785b78377e79960d0280667f98cba3305d68426fdfaf8efeecd4542d7` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs Trimmed NextSeq 150 bp paired-end reads Context-only references	Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort Original source ↗ Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', row 18; Row rank '#' as printed: 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Pathogens 11(3):340, published 2022-03-11; PMC8953373 full-text XML Retrieved: 2026-10-09T20:06:32Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `e6683855ad278a555598295fdc4166e54ddb0e39e3d971878b898b20bc8ddf95` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs Trimmed NextSeq 150 bp paired-end reads Context-only references	Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 Original source ↗ Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', row 18; Row rank '#' as printed: 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv 2022.01.21.22269647 version 1 (2022-01-21), supplementary file media-1.xlsx Retrieved: 2026-10-09T20:16:56Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `cd3a80d785b78377e79960d0280667f98cba3305d68426fdfaf8efeecd4542d7` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

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

2 source records and release history

Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort · Original source · Pathogens 11(3):340, published 2022-03-11; PMC8953373 full-text XML
Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Original source · medRxiv 2022.01.21.22269647 version 1 (2022-01-21), supplementary file media-1.xlsx

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Technical metadata and extraction receipts

Stable ID: rna-pathogen-20261009-eval-carbo2022-genus-cutoff-0-genome-detective-excl-human

areas: microbes-communities
contexts: clinical_research
origin: independent_paper
protocol: rna-pathogen-20261009-protocol-carbo2022-genus-cutoff-0
version: Primary source as retrieved 2026-10-09
comparison: protocol id: rna-pathogen-20261009-protocol-carbo2022-genus-cutoff-0; dataset version: SRX6713943-SRX6714030; split: Whole cohort; population: 88 samples, 1144 PCR results (24 positive); inputs: Trimmed NextSeq 150 bp paired-end reads; adaptation: Viral RefSeq database built 2020-12-27 (Genome Detective: own database); metric implementation: Authors' ROC analysis over read-count cut-offs; aggregation: All PCR targets pooled; budget: Not reported
source locator: Supplementary Table 1 sheet 'Suppl table 1-Genus', block 'excl. human reads', row 18; Row rank '#' as printed: 3

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