Published RNA metagenomic pathogen-detection comparison; transcribed, not reproduced.
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Release 2026-10-09-ba02f2f4a36e · Evidence verified: Not verified
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1 evaluation · 11 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: CLARK, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022) | Protocol: Respiratory virus detection against PCR, species level, read-count cut-off 10 (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) | 0.874 auroc unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcerna-pathogen-20261009-protocol-carbo2022-species-cutoff-10 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', cell S19, row 'CLARK', column 'AUC' |
| Configuration: CLARK, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022) | Protocol: Respiratory virus detection against PCR, species level, read-count cut-off 10 (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) | 33.9 regression-intercept unitless · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcerna-pathogen-20261009-protocol-carbo2022-species-cutoff-10 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', cell Y19, row 'CLARK', column 'LR intercept' |
| Configuration: CLARK, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022) | Protocol: Respiratory virus detection against PCR, species level, read-count cut-off 10 (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) | 24.1% pearson-r-squared percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcerna-pathogen-20261009-protocol-carbo2022-species-cutoff-10 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', cell Z19, row 'CLARK', column 'LR r2, %' |
| Configuration: CLARK, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022) | Protocol: Respiratory virus detection against PCR, species level, read-count cut-off 10 (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) | -1.55 regression-slope unitless · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcerna-pathogen-20261009-protocol-carbo2022-species-cutoff-10 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', cell X19, row 'CLARK', column 'LR slope' |
| Configuration: CLARK, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022) | Protocol: Respiratory virus detection against PCR, species level, read-count cut-off 10 (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) | 0.992 negative-predictive-value fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcerna-pathogen-20261009-protocol-carbo2022-species-cutoff-10 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', cell W19, row 'CLARK', column 'NPV (ROC)' |
| Configuration: CLARK, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022) | Protocol: Respiratory virus detection against PCR, species level, read-count cut-off 10 (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) | 0.9 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcerna-pathogen-20261009-protocol-carbo2022-species-cutoff-10 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', cell V19, row 'CLARK', column 'PPV (ROC)' |
| Configuration: CLARK, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022) | Protocol: Respiratory virus detection against PCR, species level, read-count cut-off 10 (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) | 0.25 roc-distance unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcerna-pathogen-20261009-protocol-carbo2022-species-cutoff-10 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', cell R19, row 'CLARK', column 'Informedness' |
| Configuration: CLARK, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022) | Protocol: Respiratory virus detection against PCR, species level, read-count cut-off 10 (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) | 0.75 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcerna-pathogen-20261009-protocol-carbo2022-species-cutoff-10 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', cell T19, row 'CLARK', column 'SN (ROC)' |
| Configuration: CLARK, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022) | Protocol: Respiratory virus detection against PCR, species level, read-count cut-off 10 (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 specificity fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcerna-pathogen-20261009-protocol-carbo2022-species-cutoff-10 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', cell U19, row 'CLARK', column 'SL (ROC)' |
| Configuration: CLARK, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022) | Protocol: Respiratory virus detection against PCR, species level, read-count cut-off 10 (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) | 17 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcerna-pathogen-20261009-protocol-carbo2022-species-cutoff-10 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', cell AA19, row 'CLARK', column 'Taxa' |
| Configuration: CLARK, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022) | Protocol: Respiratory virus detection against PCR, species level, read-count cut-off 10 (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) | 17 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcerna-pathogen-20261009-protocol-carbo2022-species-cutoff-10 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', cell AB19, row 'CLARK', column 'Taxa with reads >10' |
Source checking is not independent reproduction. Release 2026-10-09-ba02f2f4a36e.
rna-pathogen-20261009-protocol-carbo2022-species-cutoff-10
Metadata review: source checked. Unreported conditions prevent automatic comparisons.
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.
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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.
36 evidence rows matching the loaded filters
| 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 Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', row 19; Row rank '#' as printed: 5 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 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| 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 Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', row 19; Row rank '#' as printed: 5 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 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| 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 Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', row 19; Row rank '#' as printed: 5 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 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.aggregation All PCR targets pooled Context-only references | Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', row 19; Row rank '#' as printed: 5 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 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.budget Not reported Context-only references | Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', row 19; Row rank '#' as printed: 5 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 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.budget Not reported Context-only references | Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', row 19; Row rank '#' as printed: 5 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 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| 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 Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', row 19; Row rank '#' as printed: 5 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 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.dataset_version SRX6713943-SRX6714030 Context-only references | Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', row 19; Row rank '#' as printed: 5 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 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| 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 Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', row 19; Row rank '#' as printed: 5 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 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.inputs Trimmed NextSeq 150 bp paired-end reads Context-only references | Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 Supplementary Table 1 sheet 'Suppl table 1-Species', block 'excl. human reads', row 19; Row rank '#' as printed: 5 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 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-09-ba02f2f4a36e · Record review: source checked
Stable ID: rna-pathogen-20261009-eval-carbo2022-species-cutoff-10-clark-excl-human