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minimap2 Clockwork (Hall and Coin 2024)

minimap2 Clockwork as run for M. tuberculosis read classification in Hall and Coin 2024.

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minimap2 Clockwork as run for M. tuberculosis read classification in Hall and Coin 2024.

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Release 2026-10-10-7b8f80935f90 · 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-minimap2-clockwork

areas: microbes-communities
contexts: clinical_research
method types: conventional_pipeline
reported name: minimap2 Clockwork
source locator: Methods 'Mycobacterium read classification' paragraphs 2-3; minimap2 v2.26 from Methods 'Human read removal' paragraph 1
foundation model eligible: false
parameters: Clockwork decontamination database (sputum contaminants, NTM genomes, H37Rv, human) plus 17 high-quality M. tuberculosis genomes; -x map-ont or -x sr, -c --secondary=no
missing metadata: version: reason: unreported; note: Methods 'Human read removal' paragraph 1 states minimap2 v2.26 for the human read removal configuration; 'Mycobacterium read classification' does not restate a version for these runs

Related records

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: minimap2 Clockwork (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)	22.2 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 minimap2 Clockwork 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 'minimap2 Clockwork', column 'Memory (GB)†'
Configuration: minimap2 Clockwork (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)	56,485 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 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 'minimap2 Clockwork', column 'Rate (reads/s)*'
Configuration: minimap2 Clockwork (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)	0.996 recall fraction · higher Uncertainty: 95% CI 0.996 to 0.9961. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 Clockwork 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 'minimap2 Clockwork', column 'Sensitivity (95% CI)'
Configuration: minimap2 Clockwork (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 0.9996 to 0.9996. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 Clockwork 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 'minimap2 Clockwork', column 'Specificity (95% CI)'
Configuration: minimap2 Clockwork (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)	0.996 youden-index fraction · higher Uncertainty: 95% CI 0.9956 to 0.9956. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 Clockwork 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 'minimap2 Clockwork', column 'Youden’s index (95% CI)'
Configuration: minimap2 Clockwork (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)	13.8 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 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 'minimap2 Clockwork', column 'Memory (GB)†'
Configuration: minimap2 Clockwork (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)	1,225 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 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 'minimap2 Clockwork', column 'Rate (reads/s)*'
Configuration: minimap2 Clockwork (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)	0.981 recall fraction · higher Uncertainty: 95% CI 0.9799 to 0.9816. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 Clockwork 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 'minimap2 Clockwork', column 'Sensitivity (95% CI)'
Configuration: minimap2 Clockwork (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 0.9995 to 0.9996. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 Clockwork 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 'minimap2 Clockwork', column 'Specificity (95% CI)'
Configuration: minimap2 Clockwork (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)	0.98 youden-index fraction · higher Uncertainty: 95% CI 0.9794 to 0.9812. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 Clockwork 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 'minimap2 Clockwork', 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 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 checked Methods, coverage and source minimap2 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)†'
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 checked Methods, coverage and source minimap2 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)*'
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 checked Methods, coverage and source minimap2 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)'
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 checked Methods, coverage and source minimap2 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)'
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 checked Methods, coverage and source minimap2 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)'