MetageNN long-read genus classification benchmark (Peres da Silva et al. 2024)
Genus-level classification of ONT reads from bacterial isolates and pseudo-mock communities, with every tool using the same 516-genome database.
Results are recorded on the linked protocols, tasks or configurations listed below. Their settings and evaluations are kept separate.
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.
Results on linked records
This benchmark has no results of its own in this release. 3 linked records have results. They are not assigned to the underlying benchmark: each record keeps its own settings and evaluations, and its scores are on its own page.
- Genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024) Protocol · part of this benchmark · 3 evaluations · 6 results
- Read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024) Protocol · part of this benchmark · 5 evaluations · 5 results
- Database storage and classification speed on ONT data, main database (Peres da Silva et al. 2024) Protocol · part of this benchmark · 6 evaluations · 13 results
Methods and evaluation design
Procedure, tasks and evaluated configurations
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 6 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
Baseline status by linked protocol
- Genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024) · 0/2 roles measured
- Read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024) · 0/2 roles measured
- Database storage and classification speed on ONT data, main database (Peres da Silva et al. 2024) · 0/2 roles measured
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 benchmark. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Evidence
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Evidence table
Inspect claims, sources and review details
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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-benchmark
- areas
- microbes-communities
- contexts
- research
- entity level
- suite
- version
- BMC Bioinformatics 2024, Table 1 and Results prose
- task
- Assign ONT reads to their genus with or without the species genome in the reference
- source locator
- Results; Methods 'Data' and 'Databases'
- scope note
- Per-tool sensitivity, precision and F1 are shown only in Figures 3 and 4 (bar plots with values drawn on the figure) and were not read. Only values printed in the text and Table 1 are extracted. Figure 2 (GeNet and DeepMicrobes against MetageNN on the 47-genome small database) is not a baseline comparison and was not extracted.
- limitations
- The authors developed MetageNN and ran every tool.; The reference holds 516 genomes, far smaller than the databases clinical classifiers use.; Genus level only; isolates from bacteria only.
- 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
- subject: comparison_design: dna-pathogen-20261012-metagenn-benchmark
- part of: Genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024)
- part of: Read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
- part of: Database storage and classification speed on ONT data, main database (Peres da Silva et al. 2024)