| Configuration: kraken Myco (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 8.2 peak-memory gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcekraken Myco on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'kraken Myco', column 'Memory (GB)†' |
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| Configuration: kraken Myco (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 4,286 inference-throughput sample-per-second · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcekraken Myco on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'kraken Myco', column 'Rate (reads/s)*' |
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| Configuration: kraken Myco (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 0.995 recall fraction · higher Uncertainty: 95% CI 0.9947 to 0.9958. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcekraken Myco on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'kraken Myco', column 'Sensitivity (95% CI)' |
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| Configuration: kraken Myco (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 1 specificity fraction · higher Uncertainty: 95% CI 0.9998 to 1.0. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcekraken Myco on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'kraken Myco', column 'Specificity (95% CI)' |
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| Configuration: kraken Myco (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 0.995 youden-index fraction · higher Uncertainty: 95% CI 0.9945 to 0.9958. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcekraken Myco on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'kraken Myco', column 'Youden’s index (95% CI)' |
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| Configuration: kraken standard-8 (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 7.8 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-8 on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'kraken standard-8', column 'Memory (GB)†' |
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| Configuration: kraken standard-8 (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 4,884 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-8 on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'kraken standard-8', column 'Rate (reads/s)*' |
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| Configuration: kraken standard-8 (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 0.42 recall fraction · higher Uncertainty: 95% CI 0.4157 to 0.4236. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcekraken standard-8 on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'kraken standard-8', column 'Sensitivity (95% CI)' |
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| Configuration: kraken standard-8 (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 1 specificity fraction · higher Uncertainty: 95% CI 0.9999 to 1.0. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcekraken standard-8 on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'kraken standard-8', column 'Specificity (95% CI)' |
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| Configuration: kraken standard-8 (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 0.42 youden-index fraction · higher Uncertainty: 95% CI 0.4155 to 0.4236. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcekraken standard-8 on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'kraken standard-8', column 'Youden’s index (95% CI)' |
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| Configuration: kraken standard (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 66.8 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 Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'kraken standard', column 'Memory (GB)†' |
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| Configuration: kraken standard (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 1,406 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 Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'kraken standard', column 'Rate (reads/s)*' |
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| Configuration: kraken standard (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 0.741 recall fraction · higher Uncertainty: 95% CI 0.7373 to 0.7443. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcekraken standard on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'kraken standard', column 'Sensitivity (95% CI)' |
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| Configuration: kraken standard (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 1 specificity fraction · higher Uncertainty: 95% CI 0.9999 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 Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'kraken standard', column 'Specificity (95% CI)' |
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| Configuration: kraken standard (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 0.741 youden-index fraction · higher Uncertainty: 95% CI 0.7371 to 0.7443. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcekraken standard on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'kraken standard', column 'Youden’s index (95% CI)' |
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| Configuration: minimap2 Clockwork (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 14 peak-memory gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceminimap2 Clockwork on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'minimap2 Clockwork', column 'Memory (GB)†' |
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| Configuration: minimap2 Clockwork (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 349 inference-throughput sample-per-second · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceminimap2 Clockwork on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'minimap2 Clockwork', column 'Rate (reads/s)*' |
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| Configuration: minimap2 Clockwork (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 1 recall fraction · higher Uncertainty: 95% CI 0.9999 to 1.0. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceminimap2 Clockwork on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'minimap2 Clockwork', column 'Sensitivity (95% CI)' |
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| Configuration: minimap2 Clockwork (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 0.998 specificity fraction · higher Uncertainty: 95% CI 0.9978 to 0.9987. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceminimap2 Clockwork on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'minimap2 Clockwork', column 'Specificity (95% CI)' |
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| Configuration: minimap2 Clockwork (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 0.998 youden-index fraction · higher Uncertainty: 95% CI 0.9977 to 0.9987. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceminimap2 Clockwork on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'minimap2 Clockwork', column 'Youden’s index (95% CI)' |
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| Configuration: minimap2 MTB (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 2 peak-memory gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceminimap2 MTB on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'minimap2 MTB', column 'Memory (GB)†' |
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| Configuration: minimap2 MTB (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 418 inference-throughput sample-per-second · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceminimap2 MTB on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'minimap2 MTB', column 'Rate (reads/s)*' |
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| Configuration: minimap2 MTB (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 0.97 recall fraction · higher Uncertainty: 95% CI 0.969 to 0.9717. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceminimap2 MTB on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'minimap2 MTB', column 'Sensitivity (95% CI)' |
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| Configuration: minimap2 MTB (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 0.974 specificity fraction · higher Uncertainty: 95% CI 0.9715 to 0.9753. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceminimap2 MTB on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'minimap2 MTB', column 'Specificity (95% CI)' |
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| Configuration: minimap2 MTB (Hall and Coin 2024) | Protocol: M. tuberculosis read classification, simulated Nanopore (Hall and Coin 2024 Table 5)
Dataset: Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) | 0.944 youden-index fraction · higher Uncertainty: 95% CI 0.9405 to 0.9469. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceminimap2 MTB on Simulated sputum-like Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 5, row 'minimap2 MTB', column 'Youden’s index (95% CI)' |
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