Published DNA metagenomic classification comparison; transcribed, not reproduced.
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1 evaluation · 5 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: kraken standard (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, real Illumina (Hall and Coin 2024 Table 8) Dataset: Artificial real Illumina metagenome, non-human reads (Hall and Coin 2024) | 67.2 peak-memory gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcekraken standard on Artificial real Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-real-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 8, row 'kraken standard', column 'Memory (GB)†' |
| Configuration: kraken standard (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, real Illumina (Hall and Coin 2024 Table 8) Dataset: Artificial real Illumina metagenome, non-human reads (Hall and Coin 2024) | 239,420 inference-throughput sample-per-second · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcekraken standard on Artificial real Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-real-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 8, row 'kraken standard', column 'Rate (reads/s)*' |
| Configuration: kraken standard (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, real Illumina (Hall and Coin 2024 Table 8) Dataset: Artificial real Illumina metagenome, non-human reads (Hall and Coin 2024) | 0.0731 recall fraction · higher Uncertainty: 95% CI 0.073 to 0.0732. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcekraken standard on Artificial real Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-real-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 8, row 'kraken standard', column 'Sensitivity (95% CI)' |
| Configuration: kraken standard (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, real Illumina (Hall and Coin 2024 Table 8) Dataset: Artificial real Illumina metagenome, non-human reads (Hall and Coin 2024) | 1 specificity fraction · higher Uncertainty: 95% CI 1.0 to 1.0. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcekraken standard on Artificial real Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-real-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 8, row 'kraken standard', column 'Specificity (95% CI)' |
| Configuration: kraken standard (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, real Illumina (Hall and Coin 2024 Table 8) Dataset: Artificial real Illumina metagenome, non-human reads (Hall and Coin 2024) | 0.0731 youden-index fraction · higher Uncertainty: 95% CI 0.073 to 0.0732. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcekraken standard on Artificial real Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-real-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 8, row 'kraken standard', column 'Youden’s index (95% CI)' |
Source checking is not independent reproduction. Release 2026-10-09-8cc1db47c7f9.
dna-pathogen-20261009-protocol-hall2024-mtb-reads-real-illumina
Metadata review: source checked. Unreported conditions prevent automatic comparisons.
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.comparison.adaptation Database as stated per configuration Context-only references | Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Table 8, row 'kraken standard' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.aggregation All reads in the dataset Context-only references | Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Table 8, row 'kraken standard' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.budget 4 threads Context-only references | Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Table 8, row 'kraken standard' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.dataset_version Real reads combined: three 1000 Genomes individuals (NovaSeq 6000), M. tuberculosis ERR245682 (HiSeq 4000), ZymoBIOMICS D6322 ERR7255689 (MiSeq); 21,172,961 non-human read pairs (4.68 Gbp) classified Context-only references | Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Table 8, row 'kraken standard' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.inputs Non-human reads after the human read removal step Context-only references | Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Table 8, row 'kraken standard' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.metric_implementation Per-read confusion counts against known read origin Context-only references | Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Table 8, row 'kraken standard' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.population Non-human reads of the dataset Context-only references | Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Table 8, row 'kraken standard' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.protocol_id dna-pathogen-20261009-protocol-hall2024-mtb-reads-real-illumina Context-only references | Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Table 8, row 'kraken standard' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.split Single dataset Context-only references | Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Table 8, row 'kraken standard' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.origin independent_paper Context-only references | Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Table 8, row 'kraken standard' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-09-8cc1db47c7f9 · Record review: source checked
Stable ID: dna-pathogen-20261009-eval-hall2024-real-illumina-kraken2-standard