Genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024)
Per-isolate sensitivity, precision and F1 of read assignments at genus level, averaged across isolates; reported for all isolates, species in the database and species out of the database, and by number of species per genus.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
3 recorded evaluations, 6 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
3 evaluations · 6 results. Different protocols are not a single leaderboard.
Protocol: Genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024) · Dataset: ONT reads from 81 bacterial isolates (Peres da Silva et al. 2024)
Sorted by F1 (genus level; mean across all 81 isolates (species in and out of the database)) (higher 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 | F1 (genus level; mean across all 81 isolates (species in and out of the database)) | Recall (genus level; mean across all 81 isolates (species in and out of the database)) | F1 (genus level; mean across the out-of-database isolates whose genus has more than three species) | Recall (genus level; mean across the out-of-database isolates whose genus has more than three species) |
|---|---|---|---|---|
| MMseqs2 (main database, Peres da Silva et al. 2024)Evaluation | 0.85 (best in column) | 0.81 (best in column) | Not reported | Not reported |
| Kraken2 (main database, Peres da Silva et al. 2024)Evaluation | 0.83 | 0.79 | Not reported | Not reported |
| MetageNN (main database, Peres da Silva et al. 2024)Evaluation | Not reported | Not reported | 0.88 | 0.87 |
All 6 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Kraken2 (main database, Peres da Silva et al. 2024) | Protocol: Genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024) Dataset: ONT reads from 81 bacterial isolates (Peres da Silva et al. 2024) | 0.83 F1 (genus level; mean across all 81 isolates (species in and out of the database)) fraction · higher Uncertainty: Not reported by the source: Figure 3 shows standard-deviation error bars; no value is printed in the text Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcedna-pathogen-20261012-metagenn-protocol-isolates Aggregation: Not reported MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Results 'Results for all genomes' paragraph 1, sentence 4 (values shown in Fig. 3a) |
| Configuration: Kraken2 (main database, Peres da Silva et al. 2024) | Protocol: Genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024) Dataset: ONT reads from 81 bacterial isolates (Peres da Silva et al. 2024) | 0.79 Recall (genus level; mean across all 81 isolates (species in and out of the database)) fraction · higher Uncertainty: Not reported by the source: Figure 3 shows standard-deviation error bars; no value is printed in the text Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcedna-pathogen-20261012-metagenn-protocol-isolates Aggregation: Not reported MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Results 'Results for all genomes' paragraph 1, sentence 4 (values shown in Fig. 3a) |
| Configuration: MetageNN (main database, Peres da Silva et al. 2024) | Protocol: Genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024) Dataset: ONT reads from 81 bacterial isolates (Peres da Silva et al. 2024) | 0.88 F1 (genus level; mean across the out-of-database isolates whose genus has more than three species) fraction · higher Uncertainty: Not reported by the source: Figure 3 shows standard-deviation error bars; no value is printed in the text Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcedna-pathogen-20261012-metagenn-protocol-isolates Aggregation: Not reported MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Results 'Results for “Species out of the database” settings' paragraph 3, last sentences (values shown in Fig. 3f) |
| Configuration: MetageNN (main database, Peres da Silva et al. 2024) | Protocol: Genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024) Dataset: ONT reads from 81 bacterial isolates (Peres da Silva et al. 2024) | 0.87 Recall (genus level; mean across the out-of-database isolates whose genus has more than three species) fraction · higher Uncertainty: Not reported by the source: Figure 3 shows standard-deviation error bars; no value is printed in the text Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcedna-pathogen-20261012-metagenn-protocol-isolates Aggregation: Not reported MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Results 'Results for “Species out of the database” settings' paragraph 3, last sentences (values shown in Fig. 3f) |
| Configuration: MMseqs2 (main database, Peres da Silva et al. 2024) | Protocol: Genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024) Dataset: ONT reads from 81 bacterial isolates (Peres da Silva et al. 2024) | 0.85 F1 (genus level; mean across all 81 isolates (species in and out of the database)) fraction · higher Uncertainty: Not reported by the source: Figure 3 shows standard-deviation error bars; no value is printed in the text Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcedna-pathogen-20261012-metagenn-protocol-isolates Aggregation: Not reported MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Results 'Results for all genomes' paragraph 1, sentence 4 (values shown in Fig. 3a) |
| Configuration: MMseqs2 (main database, Peres da Silva et al. 2024) | Protocol: Genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024) Dataset: ONT reads from 81 bacterial isolates (Peres da Silva et al. 2024) | 0.81 Recall (genus level; mean across all 81 isolates (species in and out of the database)) fraction · higher Uncertainty: Not reported by the source: Figure 3 shows standard-deviation error bars; no value is printed in the text Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcedna-pathogen-20261012-metagenn-protocol-isolates Aggregation: Not reported MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Results 'Results for all genomes' paragraph 1, sentence 4 (values shown in Fig. 3a) |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- Kraken2 on genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024)
- MetageNN on genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024)
- MMseqs2 on genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024)
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- Author-reported evaluations
- 3
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Training-set class prior where supervised fitting is permitted
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Regularised classifier on simple permitted features, or protocol's conventional reference
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
0 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|
No evidence rows match these filters. Choose another scope or clear the search.
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Original source · BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML
Technical metadata and extraction receipts
Stable ID: dna-pathogen-20261012-metagenn-protocol-isolates
- areas
- microbes-communities
- contexts
- research
- protocol
- Per-isolate sensitivity, precision and F1 of read assignments at genus level, averaged across isolates; reported for all isolates, species in the database and species out of the database, and by number of species per genus.
- version
- BMC Bioinformatics 2024
- metric definition
- For each taxon, sensitivity is the proportion of its reads classified as such and precision the proportion of correctly classified reads; F1 is their harmonic mean. Averages are across bacterial isolates; Wilcoxon rank-sum tests compare MetageNN with each tool.
- source locator
- Results 'Evaluation metrics'; 'Results for all genomes'; 'Results for “Species out of the database” settings'
- limitations
- Most per-tool values are only in Figure 3; the text prints a few averages.
- review
- method: source-hash-verification; scope-review; reviewer: claude; reviewer note: Separate Claude review agent (rev-mlvb), independent of the extracting agent; no human review claimed; date: 2026-10-12; artifact sha256: ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11022314/fullTextXML; note: Checked against the re-downloaded article XML (SHA-256 matches).
Related records
- uses data: ONT reads from 81 bacterial isolates (Peres da Silva et al. 2024)
- part of: MetageNN long-read genus classification benchmark (Peres da Silva et al. 2024)
- subject: reported_ranking: dna-pathogen-20261012-metagenn-protocol-isolates
- subject: reported_ranking: dna-pathogen-20261012-metagenn-protocol-isolates
- assessment: Kraken2 on genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024)
- assessment: MetageNN on genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024)
- assessment: MMseqs2 on genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024)
- assessed by: Select a DNA pathogen-identification workflow for diagnostic testing