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kraken Myco (Hall and Coin 2024)

kraken Myco as run for M. tuberculosis read classification in Hall and Coin 2024.

Overview

kraken Myco as run for M. tuberculosis read classification in Hall and Coin 2024.

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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-config-hall2024-kraken2-myco

areas: microbes-communities
contexts: clinical_research
method types: conventional_pipeline
reported name: kraken Myco
source locator: Methods 'Mycobacterium read classification' paragraph 1
foundation model eligible: false
missing metadata: version: reason: unreported; note: Methods name kraken v2.1.2 only for the library download used to simulate reads; the version used for classification is not stated separately
parameters: Authors' database: one RefSeq genome per Mycobacteriaceae species plus one per species of nine other genera, downloaded with genome_updater v0.6.3 and built with kraken2-build --build; simulation genomes excluded

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: kraken Myco (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)	8.3 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 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 Myco', column 'Memory (GB)†'
Configuration: kraken Myco (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)	398,597 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 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 Myco', column 'Rate (reads/s)*'
Configuration: kraken Myco (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)	0.972 recall fraction · higher Uncertainty: 95% CI 0.9714 to 0.9716. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source kraken Myco 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 Myco', column 'Sensitivity (95% CI)'
Configuration: kraken Myco (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	Author-reported evaluation · Source checked Methods, coverage and source kraken Myco 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 Myco', column 'Specificity (95% CI)'
Configuration: kraken Myco (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)	0.972 youden-index fraction · higher Uncertainty: 95% CI 0.9714 to 0.9716. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source kraken Myco 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 Myco', column 'Youden’s index (95% CI)'
Configuration: kraken Myco (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, real Nanopore (Hall and Coin 2024 Table 6) Dataset: Artificial real 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 checked Methods, coverage and source kraken Myco on Artificial real Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-real-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 6, row 'kraken Myco', column 'Memory (GB)†'
Configuration: kraken Myco (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, real Nanopore (Hall and Coin 2024 Table 6) Dataset: Artificial real Nanopore metagenome, non-human reads (Hall and Coin 2024)	6,755 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 Artificial real Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-real-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 6, row 'kraken Myco', column 'Rate (reads/s)*'
Configuration: kraken Myco (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, real Nanopore (Hall and Coin 2024 Table 6) Dataset: Artificial real Nanopore metagenome, non-human reads (Hall and Coin 2024)	0.977 recall fraction · higher Uncertainty: 95% CI 0.9764 to 0.9782. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source kraken Myco on Artificial real Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-real-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 6, row 'kraken Myco', column 'Sensitivity (95% CI)'
Configuration: kraken Myco (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, real Nanopore (Hall and Coin 2024 Table 6) Dataset: Artificial real Nanopore 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 Artificial real Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-real-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 6, row 'kraken Myco', column 'Specificity (95% CI)'
Configuration: kraken Myco (Hall and Coin 2024)	Protocol: M. tuberculosis read classification, real Nanopore (Hall and Coin 2024 Table 6) Dataset: Artificial real Nanopore metagenome, non-human reads (Hall and Coin 2024)	0.977 youden-index fraction · higher Uncertainty: 95% CI 0.9764 to 0.9782. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source kraken Myco on Artificial real Nanopore metagenome, non-human reads (Hall and Coin 2024) dna-pathogen-20261009-protocol-hall2024-mtb-reads-real-nanopore Aggregation: Not reported Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 6, row 'kraken Myco', column 'Youden’s index (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)	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 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 checked Methods, coverage and source kraken 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)†'
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 checked Methods, coverage and source kraken 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)*'
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 checked Methods, coverage and source kraken 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)'
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 checked Methods, coverage and source kraken 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)'
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 checked Methods, coverage and source kraken 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)'