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

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

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

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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-config-carbo2022-centrifuge-excl-human

areas: microbes-communities
contexts: clinical_research
method types: conventional_pipeline
reported name: Centrifuge
source locator: Section 2.5; 2.6.1; Table 2 column 'Centrifuge'; Section 2.3 (pre-processing)
foundation model eligible: false
version: 1.0.4
parameters: Viral NCBI RefSeq genomes downloaded 2020-12-27; one label per read (lowest common ancestor) instead of the default five. Pre-processing: Trimmomatic v0.36 trimming, adapter clipping and low-complexity filtering; human reads removed (Bowtie2 to GRCh38) before classification.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Centrifuge, 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)	0.941 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 Centrifuge, 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 D19, row 'Centrifuge', column 'AUC'
Configuration: Centrifuge, 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)	35.5 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 Centrifuge, 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 J19, row 'Centrifuge', column 'LR intercept'
Configuration: Centrifuge, 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)	34.8% 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 Centrifuge, 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 K19, row 'Centrifuge', column 'LR r2, %'
Configuration: Centrifuge, 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)	-1.97 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 Centrifuge, 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 I19, row 'Centrifuge', column 'LR slope'
Configuration: Centrifuge, 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)	0.999 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 Centrifuge, 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 H19, row 'Centrifuge', column 'NPV (ROC)'
Configuration: Centrifuge, 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)	0.354 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 Centrifuge, 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 G19, row 'Centrifuge', column 'PPV (ROC)'
Configuration: Centrifuge, 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)	0.0688 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 Centrifuge, 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 C19, row 'Centrifuge', column 'Informedness'
Configuration: Centrifuge, 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)	0.958 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 Centrifuge, 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 E19, row 'Centrifuge', column 'SN (ROC)'
Configuration: Centrifuge, 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)	0.945 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 Centrifuge, 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 F19, row 'Centrifuge', column 'SL (ROC)'
Configuration: Centrifuge, 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 Centrifuge, 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 L19, row 'Centrifuge', column 'Taxa'
Configuration: Centrifuge, 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 Centrifuge, 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 M19, row 'Centrifuge', column 'Taxa with reads >0'
Configuration: Centrifuge, 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)	0.941 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 Centrifuge, 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 D19, row 'Centrifuge', column 'AUC'
Configuration: Centrifuge, 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)	35.4 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 Centrifuge, 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 J19, row 'Centrifuge', column 'LR intercept'
Configuration: Centrifuge, 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)	33.2% 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 Centrifuge, 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 K19, row 'Centrifuge', column 'LR r2, %'
Configuration: Centrifuge, 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)	-1.95 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 Centrifuge, 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 I19, row 'Centrifuge', column 'LR slope'
Configuration: Centrifuge, 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 Centrifuge, 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 H19, row 'Centrifuge', column 'NPV (ROC)'
Configuration: Centrifuge, 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)	0.564 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 Centrifuge, 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 G19, row 'Centrifuge', column 'PPV (ROC)'
Configuration: Centrifuge, 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)	0.0862 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 Centrifuge, 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 C19, row 'Centrifuge', column 'Informedness'
Configuration: Centrifuge, 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 Centrifuge, 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 E19, row 'Centrifuge', column 'SN (ROC)'
Configuration: Centrifuge, 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)	0.978 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 Centrifuge, 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 F19, row 'Centrifuge', column 'SL (ROC)'
Configuration: Centrifuge, 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 Centrifuge, 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 L19, row 'Centrifuge', column 'Taxa'
Configuration: Centrifuge, 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 Centrifuge, 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 M19, row 'Centrifuge', column 'Taxa with reads >0'
Configuration: Centrifuge, 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)	0.943 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 Centrifuge, 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 D21, row 'Centrifuge', column 'AUC'
Configuration: Centrifuge, 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)	35.2 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 Centrifuge, 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 J21, row 'Centrifuge', column 'LR intercept'
Configuration: Centrifuge, 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)	32.2% 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 Centrifuge, 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 K21, row 'Centrifuge', column 'LR r2, %'