Configuration

RIEMS as run by an ENNGS laboratory (de Vries et al. 2021)

RIEMS as used at a participating diagnostic laboratory, with its own reference database and reporting criteria.

Overview

RIEMS as used at a participating diagnostic laboratory, with its own reference database and reporting criteria.

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

Evaluations and results

2 evaluations · 23 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: RIEMS as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Virus hits against RT-PCR: true and false positives, PPV and hit-level sensitivity (de Vries et al. 2021 Supplementary Table 4) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	2 false-negative-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: virus hits against RT-PCR (ENNGS) rna-pathogen-20261009-protocol-devries2021-hit-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 4, cell Q38, row 'RIEMS', column 'FN (number of PCR-positive hits not reported by mNGS)'
Configuration: RIEMS as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Virus hits against RT-PCR: true and false positives, PPV and hit-level sensitivity (de Vries et al. 2021 Supplementary Table 4) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	3 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: virus hits against RT-PCR (ENNGS) rna-pathogen-20261009-protocol-devries2021-hit-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 4, cell O38, row 'RIEMS', column 'Number of additional viral mNGS hits with negative PCR reprsult (FP* see manuscript text for comments e.g. on index hopping)'
Configuration: RIEMS as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Virus hits against RT-PCR: true and false positives, PPV and hit-level sensitivity (de Vries et al. 2021 Supplementary Table 4) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	16 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: virus hits against RT-PCR (ENNGS) rna-pathogen-20261009-protocol-devries2021-hit-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 4, cell R38, row 'RIEMS', column 'Total mNGS hits with PCR data available (TP+FP)'
Configuration: RIEMS as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Virus hits against RT-PCR: true and false positives, PPV and hit-level sensitivity (de Vries et al. 2021 Supplementary Table 4) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	81.3% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: virus hits against RT-PCR (ENNGS) rna-pathogen-20261009-protocol-devries2021-hit-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 4, cell S38, row 'RIEMS', column 'Positive predictive value (PPV) [%]'
Configuration: RIEMS as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Virus hits against RT-PCR: true and false positives, PPV and hit-level sensitivity (de Vries et al. 2021 Supplementary Table 4) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	86.7% recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: virus hits against RT-PCR (ENNGS) rna-pathogen-20261009-protocol-devries2021-hit-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 4, cell T38, row 'RIEMS', column 'Sensitivity [%], hit level'
Configuration: RIEMS as run by an ENNGS laboratory (de Vries et al. 2021)	Protocol: Virus hits against RT-PCR: true and false positives, PPV and hit-level sensitivity (de Vries et al. 2021 Supplementary Table 4) Dataset: ENNGS benchmark: 13 clinical metagenomic datasets with RT-PCR results (de Vries et al. 2021)	13 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: virus hits against RT-PCR (ENNGS) rna-pathogen-20261009-protocol-devries2021-hit-level Aggregation: Not reported de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Supplementary Table 4, cell P38, row 'RIEMS', column 'TP (viral mNGS hits with positive PCR result, mixed infections counted as double, out of 15 positive PCRs)'
Configuration: RIEMS 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)	11 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 R69, row 'RIEMS', column 'Number of samples correctly positive ... out of 13 samples*'
Configuration: RIEMS 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	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 C69, row 'RIEMS' read count, column sample 1 (HHV-6(A))
Configuration: RIEMS 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)	29700 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 D69, row 'RIEMS' read count, column sample 2 (HHV-6(B))
Configuration: RIEMS 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)	215000 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 E69, row 'RIEMS' read count, column sample 3 (Enterovirus)
Configuration: RIEMS 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)	57600 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 F69, row 'RIEMS' read count, column sample 4 (EBV)
Configuration: RIEMS 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)	107000 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 G69, row 'RIEMS' read count, column sample 5 (Mumps)
Configuration: RIEMS 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)	180000 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 H69, row 'RIEMS' read count, column sample 6 (CoV-OC43)
Configuration: RIEMS 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)	1420 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 I69, row 'RIEMS' read count, column sample 7 (Astrovirus VA1)
Configuration: RIEMS 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)	2510 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 J69, row 'RIEMS' read count, column sample 8 (Inf-A)
Configuration: RIEMS 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)	60 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 K69, row 'RIEMS' read count, column sample 9 (PIV-3)
Configuration: RIEMS 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)	1420 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 L69, row 'RIEMS' read count, column sample 10 (CoV-NL63)
Configuration: RIEMS 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)	7630 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 M69, row 'RIEMS' read count, column sample 11 (CoV-NL63)
Configuration: RIEMS 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	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 N69, row 'RIEMS' read count, column sample 11 (CoV-HKU-1)
Configuration: RIEMS 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)	2060 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 O69, row 'RIEMS' read count, column sample 12 (CoV-HKU-1)
Configuration: RIEMS 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)	325 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 P69, row 'RIEMS' read count, column sample 13 (Adeno-virus)
Configuration: RIEMS 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)	16600 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 Q69, row 'RIEMS' read count, column sample 13 (EBV)
Configuration: RIEMS 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)	84.6% recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RIEMS: 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 S69, row 'RIEMS', column 'Overall sensitivity [%], sample level'

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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-config-devries2021-riems

areas: microbes-communities
contexts: clinical_research
method types: conventional_pipeline
reported name: RIEMS
source locator: Supplementary Table 2 cell A69; Methods 'Bioinformatic pipelines'
foundation model eligible: false
missing metadata: version: reason: unextracted; note: Pipeline details are in Table 1, which is an image in the preprint and was not transcribed
parameters: Own reference database and reporting criteria of the participating laboratory (Table 1, not transcribed)

Related records

configuration of: RIEMS
system: RIEMS: virus hits against RT-PCR (ENNGS)
system: RIEMS: sample-level detection (ENNGS)

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