Raw untrimmed datasets from patients with encephalitis, respiratory disease or fever, shared with all participants.
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Release 2026-10-09-8cc1db47c7f9 · Evidence verified: Not verified
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26 evaluations · 299 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| 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 checkedMethods, coverage and sourceCentrifuge: 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 checkedMethods, coverage and sourceCentrifuge: 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 checkedMethods, coverage and sourceCentrifuge: 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 checkedMethods, coverage and sourceCentrifuge: 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 checkedMethods, coverage and sourceCentrifuge: 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 checkedMethods, coverage and sourceCentrifuge: 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: DAMIAN 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 | Evaluation origin not reported · Source checkedMethods, coverage and sourceDAMIAN: 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 Q15, row 'DAMIAN', column 'FN (number of PCR-positive hits not reported by mNGS)' |
| Configuration: DAMIAN 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 | Evaluation origin not reported · Source checkedMethods, coverage and sourceDAMIAN: 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 O15, row 'DAMIAN', column 'Number of additional viral mNGS hits with negative PCR reprsult (FP* see manuscript text for comments e.g. on index hopping)' |
| Configuration: DAMIAN 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 | Evaluation origin not reported · Source checkedMethods, coverage and sourceDAMIAN: 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 R15, row 'DAMIAN', column 'Total mNGS hits with PCR data available (TP+FP)' |
| Configuration: DAMIAN 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 | Evaluation origin not reported · Source checkedMethods, coverage and sourceDAMIAN: 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 S15, row 'DAMIAN', column 'Positive predictive value (PPV) [%]' |
| Configuration: DAMIAN 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 | Evaluation origin not reported · Source checkedMethods, coverage and sourceDAMIAN: 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 T15, row 'DAMIAN', column 'Sensitivity [%], hit level' |
| Configuration: DAMIAN 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 | Evaluation origin not reported · Source checkedMethods, coverage and sourceDAMIAN: 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 P15, row 'DAMIAN', column 'TP (viral mNGS hits with positive PCR result, mixed infections counted as double, out of 15 positive PCRs)' |
| Configuration: DIAMOND 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 checkedMethods, coverage and sourceDIAMOND: 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 Q17, row 'DIAMOND', column 'FN (number of PCR-positive hits not reported by mNGS)' |
| Configuration: DIAMOND 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-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDIAMOND: 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 O17, row 'DIAMOND', column 'Number of additional viral mNGS hits with negative PCR reprsult (FP* see manuscript text for comments e.g. on index hopping)' |
| Configuration: DIAMOND 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceDIAMOND: 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 R17, row 'DIAMOND', column 'Total mNGS hits with PCR data available (TP+FP)' |
| Configuration: DIAMOND 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) | 92.9% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDIAMOND: 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 S17, row 'DIAMOND', column 'Positive predictive value (PPV) [%]' |
| Configuration: DIAMOND 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 checkedMethods, coverage and sourceDIAMOND: 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 T17, row 'DIAMOND', column 'Sensitivity [%], hit level' |
| Configuration: DIAMOND 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 checkedMethods, coverage and sourceDIAMOND: 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 P17, row 'DIAMOND', column 'TP (viral mNGS hits with positive PCR result, mixed infections counted as double, out of 15 positive PCRs)' |
| Configuration: DNAstar 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-negative-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNAstar: 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 Q20, row 'DNAstar', column 'FN (number of PCR-positive hits not reported by mNGS)' |
| Configuration: DNAstar 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) | 6 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNAstar: 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 O20, row 'DNAstar', column 'Number of additional viral mNGS hits with negative PCR reprsult (FP* see manuscript text for comments e.g. on index hopping)' |
| Configuration: DNAstar 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) | 21 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNAstar: 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 R20, row 'DNAstar', column 'Total mNGS hits with PCR data available (TP+FP)' |
| Configuration: DNAstar 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) | 71.4% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNAstar: 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 S20, row 'DNAstar', column 'Positive predictive value (PPV) [%]' |
| Configuration: DNAstar 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% recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNAstar: 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 T20, row 'DNAstar', column 'Sensitivity [%], hit level' |
| Configuration: DNAstar 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) | 15 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNAstar: 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 P20, row 'DNAstar', column 'TP (viral mNGS hits with positive PCR result, mixed infections counted as double, out of 15 positive PCRs)' |
| Configuration: FEVIR 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-negative-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFEVIR: 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 Q23, row 'FEVIR', column 'FN (number of PCR-positive hits not reported by mNGS)' |
Source checking is not independent reproduction. Release 2026-10-09-8cc1db47c7f9.
A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
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.
18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.access Public download at https://veb.lumc.nl/CliniMG; part also via the COMPARE Data Hub Context-only references | Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples Methods 'Datasets' paragraphs 1-3 and 'Data sharing'; Supplementary Table 2 rows 4-9 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 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) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.access Public download at https://veb.lumc.nl/CliniMG; part also via the COMPARE Data Hub Context-only references | de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 Methods 'Datasets' paragraphs 1-3 and 'Data sharing'; Supplementary Table 2 rows 4-9 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv 2021.05.04.21256618 version 1, supplementary file media-1.xlsx (sheets SuppS2, SuppS3, SuppS4) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.assay Brain biopsies: TruSeq stranded mRNA, NextSeq 500 81 bp paired; other samples: total nucleic acid with EAV and PhHV controls, NEBNext Ultra directional RNA library adapted for DNA and RNA, NextSeq 500 or NovaSeq 6000 150 bp paired; three CSF samples with vertebrate-virus capture probes; human reads removed with Bowtie2 2.3.4 Context-only references | Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples Methods 'Datasets' paragraphs 1-3 and 'Data sharing'; Supplementary Table 2 rows 4-9 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 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) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.assay Brain biopsies: TruSeq stranded mRNA, NextSeq 500 81 bp paired; other samples: total nucleic acid with EAV and PhHV controls, NEBNext Ultra directional RNA library adapted for DNA and RNA, NextSeq 500 or NovaSeq 6000 150 bp paired; three CSF samples with vertebrate-virus capture probes; human reads removed with Bowtie2 2.3.4 Context-only references | de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 Methods 'Datasets' paragraphs 1-3 and 'Data sharing'; Supplementary Table 2 rows 4-9 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv 2021.05.04.21256618 version 1, supplementary file media-1.xlsx (sheets SuppS2, SuppS3, SuppS4) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.denominator 13 Context-only references | Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples Methods 'Datasets' paragraphs 1-3 and 'Data sharing'; Supplementary Table 2 rows 4-9 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 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) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.denominator 13 Context-only references | de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 Methods 'Datasets' paragraphs 1-3 and 'Data sharing'; Supplementary Table 2 rows 4-9 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv 2021.05.04.21256618 version 1, supplementary file media-1.xlsx (sheets SuppS2, SuppS3, SuppS4) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.population 13 samples: CSF (4), brain biopsy (3), nasopharyngeal swab (3), nasal washing (1), BAL (1), plasma (1); 15 PCR-positive targets (two mixed infections), 10 RNA viruses and 5 DNA viruses (HHV-6A, HHV-6B, EBV twice, adenovirus). Context-only references | Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples Methods 'Datasets' paragraphs 1-3 and 'Data sharing'; Supplementary Table 2 rows 4-9 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 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) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.population 13 samples: CSF (4), brain biopsy (3), nasopharyngeal swab (3), nasal washing (1), BAL (1), plasma (1); 15 PCR-positive targets (two mixed infections), 10 RNA viruses and 5 DNA viruses (HHV-6A, HHV-6B, EBV twice, adenovirus). Context-only references | de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 Methods 'Datasets' paragraphs 1-3 and 'Data sharing'; Supplementary Table 2 rows 4-9 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv 2021.05.04.21256618 version 1, supplementary file media-1.xlsx (sheets SuppS2, SuppS3, SuppS4) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.source_locator Methods 'Datasets' paragraphs 1-3 and 'Data sharing'; Supplementary Table 2 rows 4-9 Context-only references | Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples Methods 'Datasets' paragraphs 1-3 and 'Data sharing'; Supplementary Table 2 rows 4-9 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 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) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.source_locator Methods 'Datasets' paragraphs 1-3 and 'Data sharing'; Supplementary Table 2 rows 4-9 Context-only references | de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 Methods 'Datasets' paragraphs 1-3 and 'Data sharing'; Supplementary Table 2 rows 4-9 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv 2021.05.04.21256618 version 1, supplementary file media-1.xlsx (sheets SuppS2, SuppS3, SuppS4) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-09-8cc1db47c7f9 · Record review: source checked
Stable ID: rna-pathogen-20261009-data-devries2021-ennngs-13-clinical