Protocol

Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2)

Each laboratory pipeline's read count for each PCR-positive target and the number of the 13 samples correctly positive.

Overview

Each laboratory pipeline's read count for each PCR-positive target and the number of the 13 samples correctly positive.

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

13 recorded evaluations, 221 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

13 evaluations · 221 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	12 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Centrifuge: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell R13, row 'Centrifuge', column 'Number of samples correctly positive ... out of 13 samples*'
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	156 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: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell C13, row 'Centrifuge' read count, column sample 1 (HHV-6(A))
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	28500 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: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell D13, row 'Centrifuge' read count, column sample 2 (HHV-6(B))
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	17800 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: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell E13, row 'Centrifuge' read count, column sample 3 (Enterovirus)
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	26400 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: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell F13, row 'Centrifuge' read count, column sample 4 (EBV)
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	81700 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: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell G13, row 'Centrifuge' read count, column sample 5 (Mumps)
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	1720000 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: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell H13, row 'Centrifuge' read count, column sample 6 (CoV-OC43)
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	1360 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: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell I13, row 'Centrifuge' read count, column sample 7 (Astrovirus VA1)
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	563 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: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell J13, row 'Centrifuge' read count, column sample 8 (Inf-A)
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	59 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: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell K13, row 'Centrifuge' read count, column sample 9 (PIV-3)
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	1400 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: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell L13, row 'Centrifuge' read count, column sample 10 (CoV-NL63)
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	7380 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: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell M13, row 'Centrifuge' read count, column sample 11 (CoV-NL63)
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	0 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: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell N13, row 'Centrifuge' read count, column sample 11 (CoV-HKU-1)
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	2080 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: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell O13, row 'Centrifuge' read count, column sample 12 (CoV-HKU-1)
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	109 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: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell P13, row 'Centrifuge' read count, column sample 13 (Adeno-virus)
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	22 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: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell Q13, row 'Centrifuge' read count, column sample 13 (EBV)
Configuration: Centrifuge as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	92.3% recall 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: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell S13, row 'Centrifuge', column 'Overall sensitivity [%], sample level'
Configuration: DAMIAN as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	10 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source DAMIAN: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell R18, row 'DAMIAN', column 'Number of samples correctly positive ... out of 13 samples*'
Configuration: DAMIAN as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	0 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source DAMIAN: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell C18, row 'DAMIAN' read count, column sample 1 (HHV-6(A))
Configuration: DAMIAN as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	31800 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source DAMIAN: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell D18, row 'DAMIAN' read count, column sample 2 (HHV-6(B))
Configuration: DAMIAN as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	232000 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source DAMIAN: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell E18, row 'DAMIAN' read count, column sample 3 (Enterovirus)
Configuration: DAMIAN as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	96 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source DAMIAN: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell F18, row 'DAMIAN' read count, column sample 4 (EBV)
Configuration: DAMIAN as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	200000 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source DAMIAN: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell G18, row 'DAMIAN' read count, column sample 5 (Mumps)
Configuration: DAMIAN as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	2350000 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source DAMIAN: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell H18, row 'DAMIAN' read count, column sample 6 (CoV-OC43)
Configuration: DAMIAN as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Detection of RT-PCR-positive viruses per sample, with assigned read counts (de Vries et al. 2021 Supplementary Table 2) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	2240 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source DAMIAN: sample-level detection (ENNGS) rna-pathogen-20261009-protocol-devries2021-sample-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 2, cell I18, row 'DAMIAN' read count, column sample 7 (Astrovirus VA1)

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Author-reported evaluations: 7
External evaluations: 5
unreported: 1

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Sources and history

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2 source records and release history

Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples · Original source · medRxiv 2021.05.04.21256618 version 1 (2021-05-08), JATS XML; published as J Clin Virol 141:104908 (doi:10.1016/j.jcv.2021.104908)
de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Original source · medRxiv 2021.05.04.21256618 version 1, supplementary file media-1.xlsx (sheets SuppS2, SuppS3, SuppS4)

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Technical metadata and extraction receipts

Stable ID: rna-pathogen-20261009-protocol-devries2021-sample-level

areas: microbes-communities
contexts: clinical_research
protocol: Participants analysed the same raw datasets blinded with their own pipelines, databases and reporting criteria. A sample counts as correctly positive when the PCR-positive virus is reported (mixed infections counted as one); sensitivity is the share of the 13 samples. Read counts are as reported, not normalised.
version: Supplementary Table 2
denominator: 13
source locator: Methods 'Bioinformatic pipelines' and 'Performance characteristics'; Supplementary Table 2
limitations: 13 samples; 5 of 15 targets are DNA viruses.; Reference databases and reporting criteria differ by laboratory.; Specimen types mixed (CSF, brain, respiratory, plasma).
missing metadata: uncertainty: reason: unreported

Related records

uses data: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)
assessment: Centrifuge: sample-level detection (ENNGS)
assessment: DAMIAN: sample-level detection (ENNGS)
assessment: DIAMOND: sample-level detection (ENNGS)
assessment: DNAstar: sample-level detection (ENNGS)
assessment: FEVIR: sample-level detection (ENNGS)
assessment: Genome Detective: sample-level detection (ENNGS)
assessment: Jovian: sample-level detection (ENNGS)
assessment: MetaMIC: sample-level detection (ENNGS)
assessment: MetaMix: sample-level detection (ENNGS)
assessment: One Codex: sample-level detection (ENNGS)
assessment: RIEMS: sample-level detection (ENNGS)
assessment: Taxonomer: sample-level detection (ENNGS)
assessment: VirMet: sample-level detection (ENNGS)
assessed by: Select an RNA pathogen-detection workflow for diagnostic testing

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