Evaluation

MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS)

Published clinical mNGS workflow comparison; transcribed, not reproduced.

Evaluation results

1 evaluation · 18 results. Different protocols are not a single leaderboard.

Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) · Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)

Sorted by False negatives (sequencing negative, comparator positive; organism level; organisms: all organisms; reference: composite reference standard (CRS)) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	False negatives (sequencing negative, comparator positive; organism level; organisms: all organisms; reference: composite reference standard (CRS))	False negatives (sequencing negative, comparator positive; organism level; organisms: bacteria; reference: composite reference standard (CRS))	False negatives (sequencing negative, comparator positive; organism level; organisms: fungi; reference: composite reference standard (CRS))	False positives (sequencing positive, comparator negative; organism level; organisms: all organisms; reference: composite reference standard (CRS))	False positives (sequencing positive, comparator negative; organism level; organisms: bacteria; reference: composite reference standard (CRS))	False positives (sequencing positive, comparator negative; organism level; organisms: fungi; reference: composite reference standard (CRS))	Recall (positive percent agreement; organism level; organisms: all organisms; reference: composite reference standard (CRS))	Recall (positive percent agreement; organism level; organisms: bacteria; reference: composite reference standard (CRS))	Recall (positive percent agreement; organism level; organisms: fungi; reference: composite reference standard (CRS))	Specificity (negative percent agreement; organism level; organisms: all organisms; reference: composite reference standard (CRS))	Specificity (negative percent agreement; organism level; organisms: bacteria; reference: composite reference standard (CRS))	Specificity (negative percent agreement; organism level; organisms: fungi; reference: composite reference standard (CRS))	True negatives (concordant negative; organism level; organisms: all organisms; reference: composite reference standard (CRS))	True negatives (concordant negative; organism level; organisms: bacteria; reference: composite reference standard (CRS))	True negatives (concordant negative; organism level; organisms: fungi; reference: composite reference standard (CRS))	True positives (concordant positive; organism level; organisms: all organisms; reference: composite reference standard (CRS))	True positives (concordant positive; organism level; organisms: bacteria; reference: composite reference standard (CRS))	True positives (concordant positive; organism level; organisms: fungi; reference: composite reference standard (CRS))
MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)Evaluation	5	3	2	13	10	4	93.3%	94%	89.5%	77.6%	83.3%	93.2%	45	50	55	70	47	17

All 18 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Metrics are recomputed from the saved predictions: not yet verified
Sample annotations are recorded: not yet verified
Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
A pinned run recipe exists: not yet verified
Compute requirements are estimated: not yet verified

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Independent validation data exist: not yet verified
Overlap with training data is checked: not yet verified

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Evaluation procedure

Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026)

Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)
Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026)
Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)

origin: Author-reported evaluation
configuration: Primary source as retrieved 2026-10-11
protocol id: dna-pathogen-20261011-hu2026-protocol-crs
dataset version: 62 residual BALF specimens (Hu et al. 2026)
split: Single clinical set
population: Organisms detected in the 62 BALF specimens by the workflow or the reference
inputs: DNA extracted from BALF
adaptation: Workflow as stated per configuration
metric implementation: Organism-level 2x2 counts; PPA and NPA
aggregation: All organism results in the specimen set
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Single clinical set
Adaptation: Workflow as stated per configuration
Scoring implementation: Organism-level 2x2 counts; PPA and NPA

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

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.

38 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Comparison: adaptation Workflow as stated per configuration Context-only references	Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy Original source ↗ Table 2, block 'NGS', column group 'Composite reference standard (CRS)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML Retrieved: 2026-10-11T21:37:24Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: adaptation Workflow as stated per configuration Context-only references	Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) Original source ↗ Table 2, block 'NGS', column group 'Composite reference standard (CRS)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: spectrum.03993-25-s0001.docx as distributed with PMC13339908 Retrieved: 2026-10-11T21:41:40Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `7ab6c2cde30619e506a5e015ef5bbb253dfa6359ebd56140577eef136b153ed9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation All organism results in the specimen set Context-only references	Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy Original source ↗ Table 2, block 'NGS', column group 'Composite reference standard (CRS)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML Retrieved: 2026-10-11T21:37:24Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation All organism results in the specimen set Context-only references	Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) Original source ↗ Table 2, block 'NGS', column group 'Composite reference standard (CRS)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: spectrum.03993-25-s0001.docx as distributed with PMC13339908 Retrieved: 2026-10-11T21:41:40Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `7ab6c2cde30619e506a5e015ef5bbb253dfa6359ebd56140577eef136b153ed9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy Original source ↗ Table 2, block 'NGS', column group 'Composite reference standard (CRS)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML Retrieved: 2026-10-11T21:37:24Z	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) Original source ↗ Table 2, block 'NGS', column group 'Composite reference standard (CRS)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: spectrum.03993-25-s0001.docx as distributed with PMC13339908 Retrieved: 2026-10-11T21:41:40Z	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `7ab6c2cde30619e506a5e015ef5bbb253dfa6359ebd56140577eef136b153ed9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version 62 residual BALF specimens (Hu et al. 2026) Context-only references	Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy Original source ↗ Table 2, block 'NGS', column group 'Composite reference standard (CRS)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML Retrieved: 2026-10-11T21:37:24Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version 62 residual BALF specimens (Hu et al. 2026) Context-only references	Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) Original source ↗ Table 2, block 'NGS', column group 'Composite reference standard (CRS)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: spectrum.03993-25-s0001.docx as distributed with PMC13339908 Retrieved: 2026-10-11T21:41:40Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `7ab6c2cde30619e506a5e015ef5bbb253dfa6359ebd56140577eef136b153ed9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs DNA extracted from BALF Context-only references	Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy Original source ↗ Table 2, block 'NGS', column group 'Composite reference standard (CRS)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML Retrieved: 2026-10-11T21:37:24Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs DNA extracted from BALF Context-only references	Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) Original source ↗ Table 2, block 'NGS', column group 'Composite reference standard (CRS)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: spectrum.03993-25-s0001.docx as distributed with PMC13339908 Retrieved: 2026-10-11T21:41:40Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `7ab6c2cde30619e506a5e015ef5bbb253dfa6359ebd56140577eef136b153ed9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

2 source records and release history

Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Original source · Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML
Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Original source · spectrum.03993-25-s0001.docx as distributed with PMC13339908

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: dna-pathogen-20261011-hu2026-eval-crs-mgi

areas: microbes-communities
contexts: clinical_research
origin: author_reported
protocol: dna-pathogen-20261011-hu2026-protocol-crs
version: Primary source as retrieved 2026-10-11
comparison: protocol id: dna-pathogen-20261011-hu2026-protocol-crs; dataset version: 62 residual BALF specimens (Hu et al. 2026); split: Single clinical set; population: Organisms detected in the 62 BALF specimens by the workflow or the reference; inputs: DNA extracted from BALF; adaptation: Workflow as stated per configuration; metric implementation: Organism-level 2x2 counts; PPA and NPA; aggregation: All organism results in the specimen set; budget: Not reported
source locator: Table 2, block 'NGS', column group 'Composite reference standard (CRS)'; Supplemental Tables S6 and S7, same block and column group
limitations: Organism-level agreement in 62 residual BALF specimens from lower respiratory tract infection; not plasma cell-free DNA and not patient-level diagnosis.; The two workflows differ in platform, library preparation, host depletion, aligner and positivity threshold together (MGISEQ-200 with BWA-MEM and RP20M >= 3; host-depleted ONT GridION with minimap2 and RP10K >= 1), so the comparison is of whole workflows, not of classifiers.; Both workflows used the same curated 20,484-genome reference database and lowest-common-ancestor assignment.; Eight of the listed authors, including co-corresponding author Lifeng Li, are affiliated with Genskey Medical Technology (Beijing), a clinical mNGS provider; the article states that the authors declare no conflict of interest. The workflows are the authors' own, so the evaluations are author_reported.

Related records

system: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)
assessment: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026)
data: 62 residual BALF specimens with culture results (Hu et al. 2026)
evaluation: hu2026 crs mgi all false-negative-count
evaluation: hu2026 crs mgi all false-positive-count
evaluation: hu2026 crs mgi all specificity
evaluation: hu2026 crs mgi all recall
evaluation: hu2026 crs mgi all true-negative-count
evaluation: hu2026 crs mgi all true-positive-count
evaluation: hu2026 crs mgi bacteria false-negative-count
evaluation: hu2026 crs mgi bacteria false-positive-count
evaluation: hu2026 crs mgi bacteria specificity
evaluation: hu2026 crs mgi bacteria recall
evaluation: hu2026 crs mgi bacteria true-negative-count
evaluation: hu2026 crs mgi bacteria true-positive-count
evaluation: hu2026 crs mgi fungi false-negative-count
evaluation: hu2026 crs mgi fungi false-positive-count
evaluation: hu2026 crs mgi fungi specificity
evaluation: hu2026 crs mgi fungi recall
evaluation: hu2026 crs mgi fungi true-negative-count
evaluation: hu2026 crs mgi fungi true-positive-count

Suggest a correction

Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	5 False negatives (sequencing negative, comparator positive; organism level; organisms: all organisms; reference: composite reference standard (CRS)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Table 2, block "NGS", column group "Composite reference standard (CRS)", row "−" (sequencing negative), column "＋" (comparator positive)
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	13 False positives (sequencing positive, comparator negative; organism level; organisms: all organisms; reference: composite reference standard (CRS)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Table 2, block "NGS", column group "Composite reference standard (CRS)", row "＋" (sequencing positive), column "−" (comparator negative)
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	77.6% Specificity (negative percent agreement; organism level; organisms: all organisms; reference: composite reference standard (CRS)) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Table 2, block "NGS", column group "Composite reference standard (CRS)", row "NPA"
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	93.3% Recall (positive percent agreement; organism level; organisms: all organisms; reference: composite reference standard (CRS)) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Table 2, block "NGS", column group "Composite reference standard (CRS)", row "PPA"
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	45 True negatives (concordant negative; organism level; organisms: all organisms; reference: composite reference standard (CRS)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Table 2, block "NGS", column group "Composite reference standard (CRS)", row "−" (sequencing negative), column "−" (comparator negative)
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	70 True positives (concordant positive; organism level; organisms: all organisms; reference: composite reference standard (CRS)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Table 2, block "NGS", column group "Composite reference standard (CRS)", row "＋" (sequencing positive), column "＋" (comparator positive)
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	3 False negatives (sequencing negative, comparator positive; organism level; organisms: bacteria; reference: composite reference standard (CRS)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 6, block "NGS", column group "Composite reference standard (CRS)", row "−" (sequencing negative), column "＋" (comparator positive)
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	10 False positives (sequencing positive, comparator negative; organism level; organisms: bacteria; reference: composite reference standard (CRS)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 6, block "NGS", column group "Composite reference standard (CRS)", row "＋" (sequencing positive), column "−" (comparator negative)
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	83.3% Specificity (negative percent agreement; organism level; organisms: bacteria; reference: composite reference standard (CRS)) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 6, block "NGS", column group "Composite reference standard (CRS)", row "NPA"
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	94% Recall (positive percent agreement; organism level; organisms: bacteria; reference: composite reference standard (CRS)) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 6, block "NGS", column group "Composite reference standard (CRS)", row "PPA"
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	50 True negatives (concordant negative; organism level; organisms: bacteria; reference: composite reference standard (CRS)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 6, block "NGS", column group "Composite reference standard (CRS)", row "−" (sequencing negative), column "−" (comparator negative)
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	47 True positives (concordant positive; organism level; organisms: bacteria; reference: composite reference standard (CRS)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 6, block "NGS", column group "Composite reference standard (CRS)", row "＋" (sequencing positive), column "＋" (comparator positive)
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	2 False negatives (sequencing negative, comparator positive; organism level; organisms: fungi; reference: composite reference standard (CRS)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 7, block "NGS", column group "Composite reference standard (CRS)", row "−" (sequencing negative), column "＋" (comparator positive)
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	4 False positives (sequencing positive, comparator negative; organism level; organisms: fungi; reference: composite reference standard (CRS)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 7, block "NGS", column group "Composite reference standard (CRS)", row "＋" (sequencing positive), column "−" (comparator negative)
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	93.2% Specificity (negative percent agreement; organism level; organisms: fungi; reference: composite reference standard (CRS)) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 7, block "NGS", column group "Composite reference standard (CRS)", row "NPA"
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	89.5% Recall (positive percent agreement; organism level; organisms: fungi; reference: composite reference standard (CRS)) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 7, block "NGS", column group "Composite reference standard (CRS)", row "PPA"
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	55 True negatives (concordant negative; organism level; organisms: fungi; reference: composite reference standard (CRS)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 7, block "NGS", column group "Composite reference standard (CRS)", row "−" (sequencing negative), column "−" (comparator negative)
Configuration: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)	Protocol: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)	17 True positives (concordant positive; organism level; organisms: fungi; reference: composite reference standard (CRS)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS) dna-pathogen-20261011-hu2026-protocol-crs Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 7, block "NGS", column group "Composite reference standard (CRS)", row "＋" (sequencing positive), column "＋" (comparator positive)