Configuration

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

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

Overview

One Codex 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: One Codex 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-negative-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source One Codex: 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 Q37, row 'One Codex', column 'FN (number of PCR-positive hits not reported by mNGS)'
Configuration: One Codex 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)	0 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source One Codex: 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 O37, row 'One Codex', column 'Number of additional viral mNGS hits with negative PCR reprsult (FP* see manuscript text for comments e.g. on index hopping)'
Configuration: One Codex 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)	12 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 One Codex: 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 R37, row 'One Codex', column 'Total mNGS hits with PCR data available (TP+FP)'
Configuration: One Codex 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)	100% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source One Codex: 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 S37, row 'One Codex', column 'Positive predictive value (PPV) [%]'
Configuration: One Codex 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)	80% 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 One Codex: 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 T37, row 'One Codex', column 'Sensitivity [%], hit level'
Configuration: One Codex 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)	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 One Codex: 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 P37, row 'One Codex', column 'TP (viral mNGS hits with positive PCR result, mixed infections counted as double, out of 15 positive PCRs)'
Configuration: One Codex 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	Independent external evaluation · Source checked Methods, coverage and source One Codex: 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 R64, row 'One Codex', column 'Number of samples correctly positive ... out of 13 samples*'
Configuration: One Codex 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 One Codex: 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 C64, row 'One Codex' read count, column sample 1 (HHV-6(A))
Configuration: One Codex 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)	4540 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 One Codex: 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 D64, row 'One Codex' read count, column sample 2 (HHV-6(B))
Configuration: One Codex 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)	8580 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 One Codex: 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 E64, row 'One Codex' read count, column sample 3 (Enterovirus)
Configuration: One Codex 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)	52400 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 One Codex: 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 F64, row 'One Codex' read count, column sample 4 (EBV)
Configuration: One Codex 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)	13500 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 One Codex: 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 G64, row 'One Codex' read count, column sample 5 (Mumps)
Configuration: One Codex 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)	296000 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 One Codex: 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 H64, row 'One Codex' read count, column sample 6 (CoV-OC43)
Configuration: One Codex 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)	174 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 One Codex: 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 I64, row 'One Codex' read count, column sample 7 (Astrovirus VA1)
Configuration: One Codex 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 One Codex: 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 J64, row 'One Codex' read count, column sample 8 (Inf-A)
Configuration: One Codex 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)	118 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 One Codex: 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 K64, row 'One Codex' read count, column sample 9 (PIV-3)
Configuration: One Codex 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)	2690 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 One Codex: 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 L64, row 'One Codex' read count, column sample 10 (CoV-NL63)
Configuration: One Codex 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)	14100 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 One Codex: 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 M64, row 'One Codex' read count, column sample 11 (CoV-NL63)
Configuration: One Codex 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 One Codex: 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 N64, row 'One Codex' read count, column sample 11 (CoV-HKU-1)
Configuration: One Codex 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)	4130 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 One Codex: 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 O64, row 'One Codex' read count, column sample 12 (CoV-HKU-1)
Configuration: One Codex 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)	541 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 One Codex: 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 P64, row 'One Codex' read count, column sample 13 (Adeno-virus)
Configuration: One Codex 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)	100 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 One Codex: 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 Q64, row 'One Codex' read count, column sample 13 (EBV)
Configuration: One Codex 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)	76.9% 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 One Codex: 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 S64, row 'One Codex', 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-one-codex

areas: microbes-communities
contexts: clinical_research
method types: conventional_pipeline
reported name: One Codex
source locator: Supplementary Table 2 cell A64; 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: One Codex
system: One Codex: virus hits against RT-PCR (ENNGS)
system: One Codex: sample-level detection (ENNGS)

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