Configuration

CLARK, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022)

CLARK on Trimmomatic-trimmed reads, human reads removed (Bowtie2 to GRCh38) before classification.

Overview

CLARK on Trimmomatic-trimmed reads, human reads removed (Bowtie2 to GRCh38) before classification.

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

Evaluations and results

4 evaluations · 44 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

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

Use this model

How it works, versions and access

Strengths, limitations and unresolved questions

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.

0 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

No evidence rows match these filters. Choose another scope or clear the search.

All evidence (JSONL) (gzip)How to read the evidence

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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: rna-pathogen-20261009-config-carbo2022-clark-excl-human

areas: microbes-communities
contexts: clinical_research
method types: conventional_pipeline
reported name: CLARK
source locator: Section 2.5; 2.6.2; Table 2 column 'Clark'; Section 2.3 (pre-processing)
foundation model eligible: false
version: 1.2.6.1
parameters: Viral NCBI RefSeq genomes downloaded 2020-12-27; default execution mode. Pre-processing: Trimmomatic v0.36 trimming, adapter clipping and low-complexity filtering; human reads removed (Bowtie2 to GRCh38) before classification.

Related records

Suggest a correction

Exact evaluated configurations and original reported results
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, family 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)	0.953 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 CLARK, human reads removed (Bowtie2 to GRCh38) before classification: family level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-family-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Family', block 'excl. human reads', cell D18, row 'CLARK', column 'AUC'
Configuration: CLARK, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022)	Protocol: Respiratory virus detection against PCR, family 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)	37.3 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 CLARK, human reads removed (Bowtie2 to GRCh38) before classification: family level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-family-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Family', block 'excl. human reads', cell J18, 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, family 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)	44.4% 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 CLARK, human reads removed (Bowtie2 to GRCh38) before classification: family level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-family-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Family', block 'excl. human reads', cell K18, 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, family 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)	-2.45 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 CLARK, human reads removed (Bowtie2 to GRCh38) before classification: family level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-family-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Family', block 'excl. human reads', cell I18, 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, family 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)	10000 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 CLARK, human reads removed (Bowtie2 to GRCh38) before classification: family level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-family-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Family', block 'excl. human reads', cell H18, 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, family 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)	0.289 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 CLARK, human reads removed (Bowtie2 to GRCh38) before classification: family level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-family-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Family', block 'excl. human reads', cell G18, 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, family 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)	0.0768 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 CLARK, human reads removed (Bowtie2 to GRCh38) before classification: family level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-family-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Family', block 'excl. human reads', cell C18, row 'CLARK', column 'Informedness'
Configuration: CLARK, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022)	Protocol: Respiratory virus detection against PCR, family 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)	10000 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 CLARK, human reads removed (Bowtie2 to GRCh38) before classification: family level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-family-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Family', block 'excl. human reads', cell E18, 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, family 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)	0.923 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 CLARK, human reads removed (Bowtie2 to GRCh38) before classification: family level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-family-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Family', block 'excl. human reads', cell F18, 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, family 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)	5 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 CLARK, human reads removed (Bowtie2 to GRCh38) before classification: family level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-family-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Family', block 'excl. human reads', cell L18, row 'CLARK', column 'Taxa'
Configuration: CLARK, human reads removed (Bowtie2 to GRCh38) before classification (Carbo et al. 2022)	Protocol: Respiratory virus detection against PCR, family 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)	5 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 CLARK, human reads removed (Bowtie2 to GRCh38) before classification: family level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-family-cutoff-0 Aggregation: Not reported Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Supplementary Table 1 sheet 'Suppl table 1-Family', block 'excl. human reads', cell M18, row 'CLARK', column 'Taxa with reads >0'
Configuration: CLARK, 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)	0.904 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 CLARK, 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 D20, row 'CLARK', column 'AUC'
Configuration: CLARK, 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)	34.3 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 CLARK, 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 J20, 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, 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)	25.1% 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 CLARK, 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 K20, 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, 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)	-1.58 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 CLARK, 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 I20, 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, 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)	0.995 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 CLARK, 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 H20, 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, 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)	0.625 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 CLARK, 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 G20, 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, 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)	0.167 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 CLARK, 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 C20, row 'CLARK', column 'Informedness'
Configuration: CLARK, 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)	0.833 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 CLARK, 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 E20, 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, 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)	0.984 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 CLARK, 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 F20, 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, 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 CLARK, 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 L20, row 'CLARK', column 'Taxa'
Configuration: CLARK, 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 CLARK, 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 M20, row 'CLARK', column 'Taxa with reads >0'
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 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)	0.906 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 CLARK, human reads removed (Bowtie2 to GRCh38) before classification: species level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-species-cutoff-0 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 D19, 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 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)	34.3 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 CLARK, human reads removed (Bowtie2 to GRCh38) before classification: species level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-species-cutoff-0 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 J19, 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 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)	29% 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 CLARK, human reads removed (Bowtie2 to GRCh38) before classification: species level, read-count cut-off 0 (Carbo et al. 2022) rna-pathogen-20261009-protocol-carbo2022-species-cutoff-0 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 K19, row 'CLARK', column 'LR r2, %'