Evaluation

MMseqs2 on read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)

Published long-read classification comparison; transcribed, not reproduced.

Evaluation results

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: MMseqs2 (main database, Peres da Silva et al. 2024)	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)	85.5% Proportion (share of reads assigned at genus level (correct or not); mean across 30 pseudo-mock communities of out-of-database species) percent · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MMseqs2 on read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024) dna-pathogen-20261012-metagenn-protocol-mocks Aggregation: Not reported MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Results 'Read classification results' paragraph 1 (values shown in Fig. 4a)

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Evaluation procedure

Read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)

Configuration: MMseqs2 (main database, Peres da Silva et al. 2024)
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)

origin: Author-reported evaluation
configuration: Primary source as retrieved 2026-10-12
protocol id: dna-pathogen-20261012-metagenn-protocol-mocks
dataset version: Read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
split: Test only
population: 30 pseudo-mocks of 20 to 34 out-of-database species, up to 100,000 reads each
inputs: ONT R9.4.1 reads
adaptation: All tools use the 516-genome main database
metric implementation: 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.
aggregation: Mean across 30 pseudo-mocks
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Test only
Adaptation: All tools use the 516-genome main database
Scoring implementation: 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.

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Evidence table

Inspect claims, sources and review details

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19 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Comparison: adaptation All tools use the 516-genome main database Context-only references	MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes Original source ↗ Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML Retrieved: 2026-10-12T20:50:20Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation Mean across 30 pseudo-mocks Context-only references	MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes Original source ↗ Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML Retrieved: 2026-10-12T20:50:20Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes Original source ↗ Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML Retrieved: 2026-10-12T20:50:20Z	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version Read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024) Context-only references	MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes Original source ↗ Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML Retrieved: 2026-10-12T20:50:20Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs ONT R9.4.1 reads Context-only references	MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes Original source ↗ Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML Retrieved: 2026-10-12T20:50:20Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: metric implementation 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. Context-only references	MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes Original source ↗ Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML Retrieved: 2026-10-12T20:50:20Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: population 30 pseudo-mocks of 20 to 34 out-of-database species, up to 100,000 reads each Context-only references	MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes Original source ↗ Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML Retrieved: 2026-10-12T20:50:20Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: protocol id dna-pathogen-20261012-metagenn-protocol-mocks Context-only references	MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes Original source ↗ Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML Retrieved: 2026-10-12T20:50:20Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: split Test only Context-only references	MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes Original source ↗ Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML Retrieved: 2026-10-12T20:50:20Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Limitations 1 values All tools were run by the MetageNN authors (author_reported). Context-only references	MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes Original source ↗ Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML Retrieved: 2026-10-12T20:50:20Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.limitations` Source artifact SHA-256: `ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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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

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Technical metadata and extraction receipts

Stable ID: dna-pathogen-20261012-metagenn-eval-mmseqs2-mocks

areas: microbes-communities
contexts: research
origin: author_reported
protocol: dna-pathogen-20261012-metagenn-protocol-mocks
version: Primary source as retrieved 2026-10-12
comparison: protocol id: dna-pathogen-20261012-metagenn-protocol-mocks; dataset version: Read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024); split: Test only; population: 30 pseudo-mocks of 20 to 34 out-of-database species, up to 100,000 reads each; inputs: ONT R9.4.1 reads; adaptation: All tools use the 516-genome main database; metric implementation: 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.; aggregation: Mean across 30 pseudo-mocks; budget: Not reported
source locator: Results 'Read classification results'; 'Community-level results'
limitations: All tools were run by the MetageNN authors (author_reported).
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).

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