Relevance of read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024) to "Select a DNA pathogen-identification workflow for diagnostic testing"
- Use case
- Select a DNA pathogen-identification workflow for diagnostic testing
- Assessed by
- Read classification on 30 ONT pseudo-mock communities of out-of-database species (Peres da Silva et al. 2024)
- Relevance
- Proxy evidence
- Endpoint
- Share of reads assigned at genus level across 30 pseudo-mocks of out-of-database species
MetageNN and the baselines Kraken2 and MEGAN-LR (on minimap2 alignments) are run on the same reads from species missing from the reference, which bears on the use case's question about organisms absent from the reference. The printed endpoint is the share of reads classified, not whether they were classified correctly. It is proxy evidence: isolate-derived reads, a 516-genome reference and genus-level calls, not patient specimens.
5 reviewed evaluations
- 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)
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.
20 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Citation locations1 values
| MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison group metagenn2024-ont Context-only references | MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison title MetageNN against alignment and k-mer classifiers on ONT reads (Peres da Silva et al. 2024) Context-only references | MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints2 values
| MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Endpoint Share of reads assigned at genus level across 30 pseudo-mocks of out-of-database species Context-only references | MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field links:assessed_by:dna-pathogen-20261012-metagenn-protocol-mocks Context-only references | MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Headline metric proportion Context-only references | MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Limitations7 values
| MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records13 values
| MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Rationale MetageNN and the baselines Kraken2 and MEGAN-LR (on minimap2 alignments) are run on the same reads from species missing from the reference, which bears on the use case's question about organisms absent from the reference. The printed endpoint is the share of reads classified, not whether they were classified correctly. It is proxy evidence: isolate-derived reads, a 516-genome reference and genus-level calls, not patient specimens. Context-only references | MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes dna-pathogen-20261012-metagenn-source: Results 'Read classification results'; 'Community-level results' Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
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: use-case-mapping-dna-pathogen-20261012-metagenn-mocks
- field
- links:assessed_by:dna-pathogen-20261012-metagenn-protocol-mocks
- value
- dna-pathogen-20261012-metagenn-protocol-mocks
- relevance
- proxy
- endpoint
- Share of reads assigned at genus level across 30 pseudo-mocks of out-of-database species
- rationale
- MetageNN and the baselines Kraken2 and MEGAN-LR (on minimap2 alignments) are run on the same reads from species missing from the reference, which bears on the use case's question about organisms absent from the reference. The printed endpoint is the share of reads classified, not whether they were classified correctly. It is proxy evidence: isolate-derived reads, a 516-genome reference and genus-level calls, not patient specimens.
- constraints
- Inspect every linked evaluation's source locator and preserved limitations before citing a result.; Do not combine these results with another protocol's results; references and taxonomic ranks differ between sources.
- limitations
- Most per-tool accuracy values are only in Figures 3 and 4 and were not extracted.; Bacterial isolates only; no host DNA, viruses, fungi or clinical specimens.; A 516-genome reference and genus-level classification.; minimap2 is used only to produce MEGAN-LR's alignments, not scored on its own.; The pseudo-mocks are assembled in silico from isolate reads; they are not sequenced communities.; A larger share of reads assigned is not better by itself; whether the assignments were correct is shown only in Figure 4b.; All tools were run by the MetageNN authors, who developed MetageNN (author_reported); no uncertainty is printed.
- citation locators
- source id: dna-pathogen-20261012-metagenn-source; locator: Results 'Read classification results'; 'Community-level results'
- source locator
- dna-pathogen-20261012-metagenn-source: Results 'Read classification results'; 'Community-level results'
- revision
- 1
- reason
- Drafted by the extracting agent in the 2026-10-12 ML-versus-baseline pass (issue #121); reviewed by a separate Claude review agent on 2026-10-12 with corrections (docs/reviews/use-cases/dna-pathogen-ml-baseline-2026-10-12.md).
- comparison group
- metagenn2024-ont
- comparison title
- MetageNN against alignment and k-mer classifiers on ONT reads (Peres da Silva et al. 2024)
- headline metric
- proportion
- stratum label
- Pseudo-mock communities of out-of-database species
- stratum order
- 2
- review
- method: source-hash-verification; independent-cell-check; 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; method note: Judgement drafted by the extracting agent from the pinned article.; note: Endpoint, proxy relevance and limitations checked against the use case's question, inputs and baseline. Every result on the listed evaluations was checked against the article XML.
- reviewed evaluations
- dna-pathogen-20261012-metagenn-eval-kraken2-mocks; dna-pathogen-20261012-metagenn-eval-megan-lr-mocks; dna-pathogen-20261012-metagenn-eval-metagenn-mocks; dna-pathogen-20261012-metagenn-eval-metamaps-mocks; dna-pathogen-20261012-metagenn-eval-mmseqs2-mocks
- pins
- record id: dna-pathogen-20261012-metagenn-eval-kraken2-mocks; fields: status; links; attributes.origin; attributes.comparison; sha256: cd07224ce597ca6c4456a2e1a81dfb5942f0cd8541f0104f9b3e0356ec9ac659; record id: dna-pathogen-20261012-metagenn-eval-megan-lr-mocks; fields: status; links; attributes.origin; attributes.comparison; sha256: 84e4ee2adf909dad93656577276517bbc306cc5fd275c432052d19c7bad8d8c3; record id: dna-pathogen-20261012-metagenn-eval-metagenn-mocks; fields: status; links; attributes.origin; attributes.comparison; sha256: 81b1706415911dcdd9b0f023130e2a33b0588ccd2422855caaf92cb6d2ce5ed9; record id: dna-pathogen-20261012-metagenn-eval-metamaps-mocks; fields: status; links; attributes.origin; attributes.comparison; sha256: b35e97982908687453502a4765460bf7a428bd1e2c5bd29c30a16579a85f6536; record id: dna-pathogen-20261012-metagenn-eval-mmseqs2-mocks; fields: status; links; attributes.origin; attributes.comparison; sha256: 2185a4ade3d55aee6efcdba5e1cb60f32052521e455ff0bf6891ff0563798400; record id: dna-pathogen-20261012-metagenn-protocol-mocks; fields: status; name; description; facets; source_ids; links; attributes; sha256: 73b04bcc76cf3c7a7c0311b12c3e16199dddb2523392f3d419c42b7264bb8ef6; record id: dna-pathogen-20261012-metagenn-result-kraken2-mocks-reads-classified; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: b8a486344904a3559835a86ba02df30c69840b552b8f70e7d027f8c49bccce78; record id: dna-pathogen-20261012-metagenn-result-megan-lr-mocks-reads-classified; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: befae99b0e38d0a7bd690f8dd57be0b1068c3934717eac22e5bd94bc7a78c070; record id: dna-pathogen-20261012-metagenn-result-metagenn-mocks-reads-classified; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 3619860267f3f8fd0ae166425ec3b0b93e8091829ca2346a304a8404a284a522; record id: dna-pathogen-20261012-metagenn-result-metamaps-mocks-reads-classified; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 37ec5c2025b071983f87747ad82a39447277df8eae438936ce272cb889e82b8c; record id: dna-pathogen-20261012-metagenn-result-mmseqs2-mocks-reads-classified; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 31ce21a191ea402ae48f3f3a69ae6d6a98c116991ce243ef406e931c283970c3; record id: dna-pathogen-20261012-metagenn-source; fields: status; attributes.artifact_sha256; sha256: e8ab45945d6be94b2b510f47fec3f8847c209fbee7309ad4cfdd841f4ff6a331; record id: use-case-diagnostic-dna-pathogen-identification; fields: status; name; description; facets; attributes.question; attributes.decision; attributes.inputs; attributes.output; attributes.exclusions; attributes.setting; attributes.clinical_scope; attributes.intended_users; sha256: fc133441f475bb23dafd0c0c55f4e16cd20302f9148b21b98de31077dfe16338