Protocol

M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7)

Per-read sensitivity, specificity and Youden's index for classifying non-human reads as M. tuberculosis, with throughput and peak memory.

6 evaluations · 30 results

Overview

Per-read sensitivity, specificity and Youden's index for classifying non-human reads as M. tuberculosis, with throughput and peak memory.

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6 recorded evaluations, 30 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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6 evaluations · 30 results. Different protocols are not a single leaderboard.

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Author-reported evaluations: 4
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Sources and history

Release 2026-10-09-8cc1db47c7f9 · Record review: source checked

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Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Original source · GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML

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Technical metadata and extraction receipts

Stable ID: dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina

areas: microbes-communities
contexts: clinical_research
protocol: True positive: a read from an M. tuberculosis genome classified as M. tuberculosis; true negative: a non-M. tuberculosis read not so classified; false positive: a non-M. tuberculosis read classified as M. tuberculosis; false negative: an M. tuberculosis read not so classified. Sensitivity, specificity and Youden's index with 95% Wilson score intervals; rate is the mean and memory the maximum of 10 executions on 4 threads.
version: Table 7
source locator: Methods 'Human read removal' paragraph 4 and 'Mycobacterium read classification' paragraph 4
limitations: Read-level metrics; a sample-level detection call is not evaluated.; One target pathogen (M. tuberculosis); NTM reads are negatives.; Three of the six configurations use databases built by the authors.

Related records

Suggest a correction

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: kraken Myco (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina 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 checked Methods, coverage and source kraken Myco on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'kraken Myco', column 'Memory (GB)†'
Configuration: kraken Myco (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	194,893 inference-throughput sample-per-second · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source kraken Myco on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'kraken Myco', column 'Rate (reads/s)*'
Configuration: kraken Myco (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	0.973 recall fraction · higher Uncertainty: 95% CI 0.9726 to 0.9737. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source kraken Myco on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'kraken Myco', column 'Sensitivity (95% CI)'
Configuration: kraken Myco (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like 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	Author-reported evaluation · Source checked Methods, coverage and source kraken Myco on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'kraken Myco', column 'Specificity (95% CI)'
Configuration: kraken Myco (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	0.973 youden-index fraction · higher Uncertainty: 95% CI 0.9726 to 0.9737. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source kraken Myco on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'kraken Myco', column 'Youden’s index (95% CI)'
Configuration: kraken standard-8 (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	7.7 peak-memory gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source kraken standard-8 on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'kraken standard-8', column 'Memory (GB)†'
Configuration: kraken standard-8 (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	193,794 inference-throughput sample-per-second · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source kraken standard-8 on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'kraken standard-8', column 'Rate (reads/s)*'
Configuration: kraken standard-8 (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	0.0548 recall fraction · higher Uncertainty: 95% CI 0.0541 to 0.0556. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source kraken standard-8 on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'kraken standard-8', column 'Sensitivity (95% CI)'
Configuration: kraken standard-8 (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like 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 checked Methods, coverage and source kraken standard-8 on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'kraken standard-8', column 'Specificity (95% CI)'
Configuration: kraken standard-8 (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	0.0548 youden-index fraction · higher Uncertainty: 95% CI 0.0541 to 0.0556. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source kraken standard-8 on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'kraken standard-8', column 'Youden’s index (95% CI)'
Configuration: kraken standard (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina 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 checked Methods, coverage and source kraken standard on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'kraken standard', column 'Memory (GB)†'
Configuration: kraken standard (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	51,079 inference-throughput sample-per-second · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source kraken standard on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'kraken standard', column 'Rate (reads/s)*'
Configuration: kraken standard (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	0.163 recall fraction · higher Uncertainty: 95% CI 0.1622 to 0.1647. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source kraken standard on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'kraken standard', column 'Sensitivity (95% CI)'
Configuration: kraken standard (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like 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 checked Methods, coverage and source kraken standard on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'kraken standard', column 'Specificity (95% CI)'
Configuration: kraken standard (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	0.163 youden-index fraction · higher Uncertainty: 95% CI 0.1622 to 0.1647. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source kraken standard on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'kraken standard', column 'Youden’s index (95% CI)'
Configuration: minimap2 Clockwork (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	20.7 peak-memory gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 Clockwork on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'minimap2 Clockwork', column 'Memory (GB)†'
Configuration: minimap2 Clockwork (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	29,100 inference-throughput sample-per-second · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 Clockwork on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'minimap2 Clockwork', column 'Rate (reads/s)*'
Configuration: minimap2 Clockwork (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina 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 checked Methods, coverage and source minimap2 Clockwork on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'minimap2 Clockwork', column 'Sensitivity (95% CI)'
Configuration: minimap2 Clockwork (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	1 specificity fraction · higher Uncertainty: 95% CI 0.9999 to 0.9999. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 Clockwork on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'minimap2 Clockwork', column 'Specificity (95% CI)'
Configuration: minimap2 Clockwork (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	1 youden-index fraction · higher Uncertainty: 95% CI 0.9998 to 0.9999. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 Clockwork on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'minimap2 Clockwork', column 'Youden’s index (95% CI)'
Configuration: minimap2 MTB (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	0.7 peak-memory gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 MTB on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'minimap2 MTB', column 'Memory (GB)†'
Configuration: minimap2 MTB (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	91,734 inference-throughput sample-per-second · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 MTB on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'minimap2 MTB', column 'Rate (reads/s)*'
Configuration: minimap2 MTB (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	0.948 recall fraction · higher Uncertainty: 95% CI 0.9467 to 0.9482. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 MTB on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'minimap2 MTB', column 'Sensitivity (95% CI)'
Configuration: minimap2 MTB (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	0.999 specificity fraction · higher Uncertainty: 95% CI 0.999 to 0.9991. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 MTB on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'minimap2 MTB', column 'Specificity (95% CI)'
Configuration: minimap2 MTB (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7) Dataset: Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)	0.947 youden-index fraction · higher Uncertainty: 95% CI 0.9457 to 0.9473. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 MTB on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'minimap2 MTB', column 'Youden’s index (95% CI)'