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kraken standard (Hall and Coin 2024)

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

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kraken standard 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-standard

areas: microbes-communities
contexts: clinical_research
method types: conventional_pipeline
reported name: kraken standard
source locator: Methods 'Mycobacterium read classification' paragraphs 1 and 3
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: Kraken standard database (complete RefSeq bacteria, archaea, viruses, human genome and vectors), built 2023-06-05; default options (--paired for Illumina)

Related records

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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 checked Methods, coverage and source kraken 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 checked Methods, coverage and source kraken 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 checked Methods, coverage and source kraken 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 checked Methods, coverage and source kraken 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 checked Methods, coverage and source kraken 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)'
Configuration: kraken standard (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)	67 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 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 standard', column 'Memory (GB)†'
Configuration: kraken standard (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)	6740 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 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 standard', column 'Rate (reads/s)*'
Configuration: kraken standard (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)	0.711 recall fraction · higher Uncertainty: 95% CI 0.7086 to 0.7142. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source kraken standard 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 standard', column 'Sensitivity (95% CI)'
Configuration: kraken standard (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	Independent external evaluation · Source checked Methods, coverage and source kraken standard 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 standard', column 'Specificity (95% CI)'
Configuration: kraken standard (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)	0.711 youden-index fraction · higher Uncertainty: 95% CI 0.7086 to 0.7142. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source kraken standard 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 standard', 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: 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 checked Methods, coverage and source kraken 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)†'
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 checked Methods, coverage and source kraken 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)*'
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 checked Methods, coverage and source kraken 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)'
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 checked Methods, coverage and source kraken 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)'
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 checked Methods, coverage and source kraken 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)'