Configuration
Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)
Host-depleted ONT GridION mNGS workflow, a configuration of Harmonised mNGS analysis workflow: Host depletion with heat-labile salt-active nuclease and saponin, 17,000 x g centrifugation, bead beating and the same DNA extraction kit; ONT Rapid PCR Barcoding Kit SQK-RPB004.
Overview
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Evaluations and results
3 evaluations · 54 results. Different protocols are not a single leaderboard.
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: clinical microbiological tests (CMT)) (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 | Protocol and dataset | False negatives (sequencing negative, comparator positive; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT)) | 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: all organisms; reference: routine culture) | False negatives (sequencing negative, comparator positive; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT)) | False negatives (sequencing negative, comparator positive; organism level; organisms: bacteria; reference: composite reference standard (CRS)) | False negatives (sequencing negative, comparator positive; organism level; organisms: bacteria; reference: routine culture) | False negatives (sequencing negative, comparator positive; organism level; organisms: fungi; reference: clinical microbiological tests (CMT)) | False negatives (sequencing negative, comparator positive; organism level; organisms: fungi; reference: composite reference standard (CRS)) | False negatives (sequencing negative, comparator positive; organism level; organisms: fungi; reference: routine culture) | False positives (sequencing positive, comparator negative; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT)) | 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: all organisms; reference: routine culture) | False positives (sequencing positive, comparator negative; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT)) | False positives (sequencing positive, comparator negative; organism level; organisms: bacteria; reference: composite reference standard (CRS)) | False positives (sequencing positive, comparator negative; organism level; organisms: bacteria; reference: routine culture) | False positives (sequencing positive, comparator negative; organism level; organisms: fungi; reference: clinical microbiological tests (CMT)) | False positives (sequencing positive, comparator negative; organism level; organisms: fungi; reference: composite reference standard (CRS)) | False positives (sequencing positive, comparator negative; organism level; organisms: fungi; reference: routine culture) | Recall (positive percent agreement; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT)) | Recall (positive percent agreement; organism level; organisms: all organisms; reference: composite reference standard (CRS)) | Recall (positive percent agreement; organism level; organisms: all organisms; reference: routine culture) | Recall (positive percent agreement; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT)) | Recall (positive percent agreement; organism level; organisms: bacteria; reference: composite reference standard (CRS)) | Recall (positive percent agreement; organism level; organisms: fungi; reference: clinical microbiological tests (CMT)) | Recall (positive percent agreement; organism level; organisms: fungi; reference: composite reference standard (CRS)) | Recall (sensitivity; organism level; organisms: bacteria; reference: routine culture) | Recall (sensitivity; organism level; organisms: fungi; reference: routine culture) | Specificity (negative percent agreement; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT)) | Specificity (negative percent agreement; organism level; organisms: all organisms; reference: composite reference standard (CRS)) | Specificity (negative percent agreement; organism level; organisms: all organisms; reference: routine culture) | Specificity (negative percent agreement; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT)) | Specificity (negative percent agreement; organism level; organisms: bacteria; reference: composite reference standard (CRS)) | Specificity (negative percent agreement; organism level; organisms: fungi; reference: clinical microbiological tests (CMT)) | Specificity (negative percent agreement; organism level; organisms: fungi; reference: composite reference standard (CRS)) | Specificity (specificity; organism level; organisms: bacteria; reference: routine culture) | Specificity (specificity; organism level; organisms: fungi; reference: routine culture) | True negatives (concordant negative; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT)) | True negatives (concordant negative; organism level; organisms: all organisms; reference: composite reference standard (CRS)) | True negatives (concordant negative; organism level; organisms: all organisms; reference: routine culture) | True negatives (concordant negative; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT)) | True negatives (concordant negative; organism level; organisms: bacteria; reference: composite reference standard (CRS)) | True negatives (concordant negative; organism level; organisms: bacteria; reference: routine culture) | True negatives (concordant negative; organism level; organisms: fungi; reference: clinical microbiological tests (CMT)) | True negatives (concordant negative; organism level; organisms: fungi; reference: composite reference standard (CRS)) | True negatives (concordant negative; organism level; organisms: fungi; reference: routine culture) | True positives (concordant positive; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT)) | True positives (concordant positive; organism level; organisms: all organisms; reference: composite reference standard (CRS)) | True positives (concordant positive; organism level; organisms: all organisms; reference: routine culture) | True positives (concordant positive; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT)) | True positives (concordant positive; organism level; organisms: bacteria; reference: composite reference standard (CRS)) | True positives (concordant positive; organism level; organisms: bacteria; reference: routine culture) | True positives (concordant positive; organism level; organisms: fungi; reference: clinical microbiological tests (CMT)) | True positives (concordant positive; organism level; organisms: fungi; reference: composite reference standard (CRS)) | True positives (concordant positive; organism level; organisms: fungi; reference: routine culture) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)Evaluation | Organism-level agreement with clinical microbiological tests (CMT), 62 BALF specimens (Hu et al. 2026) | 7 | Not reported | Not reported | 4 | Not reported | Not reported | 3 | Not reported | Not reported | 10 | Not reported | Not reported | 5 | Not reported | Not reported | 5 | Not reported | Not reported | 84.1% | Not reported | Not reported | 86.2% | Not reported | 76.9% | Not reported | Not reported | Not reported | 79.2% | Not reported | Not reported | 88.9% | Not reported | 91.2% | Not reported | Not reported | Not reported | 42 | Not reported | Not reported | 40 | Not reported | Not reported | 52 | Not reported | Not reported | 37 | Not reported | Not reported | 25 | Not reported | Not reported | 10 | Not reported | Not reported |
| Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)Evaluation | Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) | Not reported | 7 | Not reported | Not reported | 4 | Not reported | Not reported | 3 | Not reported | Not reported | 10 | Not reported | Not reported | 5 | Not reported | Not reported | 5 | Not reported | Not reported | 90.7% | Not reported | Not reported | 92% | Not reported | 84.2% | Not reported | Not reported | Not reported | 83.3% | Not reported | Not reported | 91.2% | Not reported | 91.7% | Not reported | Not reported | Not reported | 50 | Not reported | Not reported | 52 | Not reported | Not reported | 55 | Not reported | Not reported | 68 | Not reported | Not reported | 46 | Not reported | Not reported | 16 | Not reported |
| Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)Evaluation | Organism-level agreement with routine culture, 62 BALF specimens (Hu et al. 2026) | Not reported | Not reported | 1 | Not reported | Not reported | 1 | Not reported | Not reported | 0 | Not reported | Not reported | 30 | Not reported | Not reported | 24 | Not reported | Not reported | 11 | Not reported | Not reported | 95.2% | Not reported | Not reported | Not reported | Not reported | 93.3% | 100% | Not reported | Not reported | 46.4% | Not reported | Not reported | Not reported | Not reported | 57.1% | 81.4% | Not reported | Not reported | 26 | Not reported | Not reported | 32 | Not reported | Not reported | 48 | Not reported | Not reported | 20 | Not reported | Not reported | 14 | Not reported | Not reported | 4 |
All 54 result rows with coverage, uncertainty and sources
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Evidence
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record 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
Technical metadata and extraction receipts
Stable ID: dna-pathogen-20261011-hu2026-config-hdont
- areas
- microbes-communities
- contexts
- clinical_research
- method types
- conventional_pipeline
- reported name
- TGS (HD-ONT)
- source locator
- Methods 'TGS workflows', 'Bioinformatic processing and taxonomic assignment' and 'Read normalization, reporting threshold, and contamination control'; Results 'Diagnostic performance for clinical samples' paragraph 1
- foundation model eligible
- false
- parameters
- Host depletion with heat-labile salt-active nuclease and saponin, 17,000 x g centrifugation, bead beating and the same DNA extraction kit; ONT Rapid PCR Barcoding Kit SQK-RPB004; GridION X5 with R9.4.1 flow cells; Guppy basecalling; reads Q > 7 and > 200 bp; minimap2 host removal and alignment to the curated database; LCA; positive if RP10K >= 1; same contamination filter
- access reuse
- Laboratory workflow described in the article; not released as software
- missing metadata
- version: reason: unreported; note: Guppy, Bowtie2, BWA-MEM and minimap2 versions and the database build date are not stated
- provenance note
- TGS (HD-ONT) as run on the clinical BALF specimens in Hu et al. 2026.
Related records
- configuration of: Harmonised mNGS analysis workflow (Hu et al. 2026)
- system: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT)
- system: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against composite reference standard (CRS)
- system: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against routine culture