Configuration

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

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

Overview

Centrifuge 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.

Filter evaluations

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: 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)	1 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 Centrifuge: 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 Q10, row 'Centrifuge', column 'FN (number of PCR-positive hits not reported by mNGS)'
Configuration: Centrifuge 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 Centrifuge: 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 O10, row 'Centrifuge', column 'Number of additional viral mNGS hits with negative PCR reprsult (FP* see manuscript text for comments e.g. on index hopping)'
Configuration: Centrifuge 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)	14 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: 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 R10, row 'Centrifuge', column 'Total mNGS hits with PCR data available (TP+FP)'
Configuration: Centrifuge 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 Centrifuge: 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 S10, row 'Centrifuge', column 'Positive predictive value (PPV) [%]'
Configuration: Centrifuge 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)	93.3% 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: 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 T10, row 'Centrifuge', column 'Sensitivity [%], hit level'
Configuration: Centrifuge 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)	14 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: 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 P10, row 'Centrifuge', column 'TP (viral mNGS hits with positive PCR result, mixed infections counted as double, out of 15 positive PCRs)'
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'

Source checking is not independent reproduction. Release 2026-10-09-ba02f2f4a36e.

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-ba02f2f4a36e
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-ba02f2f4a36e · Record review: source checked

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)

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: rna-pathogen-20261009-config-devries2021-centrifuge

areas: microbes-communities
contexts: clinical_research
method types: conventional_pipeline
reported name: Centrifuge
source locator: Supplementary Table 2 cell A13; 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: Centrifuge
system: Centrifuge: virus hits against RT-PCR (ENNGS)
system: Centrifuge: sample-level detection (ENNGS)

Suggest a correction