Read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
Average percentage of reads classified at genus level per tool across the 30 pseudo-mocks; community-level sensitivity, precision and F1 at 0.001, 0.1 and 1% thresholds appear only in Figure 4b.
Overview
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5 recorded evaluations, 5 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
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All evaluations
5 evaluations · 5 results. Different protocols are not a single leaderboard.
Protocol: Read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024) · Dataset: 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
In source order. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Proportion (share of reads assigned at genus level (correct or not); mean across 30 pseudo-mock communities of out-of-database species) |
|---|---|
| Kraken2 (main database, Peres da Silva et al. 2024)Evaluation | 64.9% |
| MEGAN-LR (main database, Peres da Silva et al. 2024)Evaluation | 53.1% |
| MetageNN (main database, Peres da Silva et al. 2024)Evaluation | 93.3% |
| MetaMaps (main database, Peres da Silva et al. 2024)Evaluation | 37.3% |
| MMseqs2 (main database, Peres da Silva et al. 2024)Evaluation | 85.5% |
All 5 result rows with coverage, uncertainty and sources
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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 read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
- MEGAN-LR on read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
- MetageNN on read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
- MetaMaps on read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
- MMseqs2 on read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
Baseline coverage
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- Author-reported evaluations
- 5
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Null control
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Regularised classifier on simple permitted features, or protocol's conventional reference
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Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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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-protocol-mocks
- areas
- microbes-communities
- contexts
- research
- protocol
- Average percentage of reads classified at genus level per tool across the 30 pseudo-mocks; community-level sensitivity, precision and F1 at 0.001, 0.1 and 1% thresholds appear only in Figure 4b.
- version
- BMC Bioinformatics 2024
- metric definition
- Read classification: percentage of reads assigned at genus level, whether or not correctly. Community level: presence of a genus above a cumulative read-count threshold.
- source locator
- Results 'Read classification results'; 'Community-level results'
- limitations
- Reads classified is not accuracy: a classified read may be assigned to the wrong genus.
- 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: 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
- part of: MetageNN long-read genus classification benchmark (Peres da Silva et al. 2024)
- assessment: Kraken2 on read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
- assessment: MEGAN-LR on read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
- assessment: MetageNN on read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
- assessment: MetaMaps on read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
- assessment: MMseqs2 on read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
- assessed by: Select a DNA pathogen-identification workflow for diagnostic testing