Configuration
MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)
MGISEQ-200 short-read mNGS workflow, a configuration of Harmonised mNGS analysis workflow: NGS (MGI platform).
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) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)Evaluation | Organism-level agreement with clinical microbiological tests (CMT), 62 BALF specimens (Hu et al. 2026) | 5 | Not reported | Not reported | 3 | Not reported | Not reported | 2 | Not reported | Not reported | 13 | Not reported | Not reported | 10 | Not reported | Not reported | 4 | Not reported | Not reported | 88.6% | Not reported | Not reported | 89.7% | Not reported | 84.6% | Not reported | Not reported | Not reported | 75% | Not reported | Not reported | 80% | Not reported | 92.9% | Not reported | Not reported | Not reported | 39 | Not reported | Not reported | 40 | Not reported | Not reported | 52 | Not reported | Not reported | 39 | Not reported | Not reported | 26 | Not reported | Not reported | 11 | Not reported | Not reported |
| MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)Evaluation | Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) | Not reported | 5 | Not reported | Not reported | 3 | Not reported | Not reported | 2 | Not reported | Not reported | 13 | Not reported | Not reported | 10 | Not reported | Not reported | 4 | Not reported | Not reported | 93.3% | Not reported | Not reported | 94% | Not reported | 89.5% | Not reported | Not reported | Not reported | 77.6% | Not reported | Not reported | 83.3% | Not reported | 93.2% | Not reported | Not reported | Not reported | 45 | Not reported | Not reported | 50 | Not reported | Not reported | 55 | Not reported | Not reported | 70 | Not reported | Not reported | 47 | Not reported | Not reported | 17 | Not reported |
| MGISEQ-200 short-read 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 | 31 | Not reported | Not reported | 26 | Not reported | Not reported | 8 | Not reported | Not reported | 95.2% | Not reported | Not reported | Not reported | Not reported | 93.3% | 100% | Not reported | Not reported | 44.6% | Not reported | Not reported | Not reported | Not reported | 54.4% | 85.7% | Not reported | Not reported | 25 | Not reported | Not reported | 31 | 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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Strengths, limitations and unresolved questions
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-mgi
- areas
- microbes-communities
- contexts
- clinical_research
- method types
- conventional_pipeline
- reported name
- NGS (MGI platform)
- source locator
- Methods 'NGS 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
- Bead beating and TIANGEN Microsample Genomic DNA extraction; VAHTS Universal Plus DNA library for MGI; MGISEQ-200 single-end 50 bp; DUST and quality filtering; Bowtie2 host removal against GRCh38 plus plasmids; BWA-MEM to the curated database; LCA; positive if RP20M >= 3; contaminants flagged above the 95th percentile of historical negative controls
- 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
- NGS (MGI platform) 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: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT)
- system: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against composite reference standard (CRS)
- system: MGISEQ-200 short-read mNGS workflow (Hu et al. 2026) against routine culture