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minimap2 Myco (Hall and Coin 2024)

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

Overview

minimap2 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-minimap2-myco

areas: microbes-communities
contexts: clinical_research
method types: conventional_pipeline
reported name: minimap2 Myco
source locator: Methods 'Mycobacterium read classification' paragraphs 2-3
foundation model eligible: false
parameters: Authors' database: one RefSeq genome per leaf node of the Mycobacterium genus plus the 17 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

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: minimap2 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)	12.9 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 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 'minimap2 Myco', column 'Memory (GB)†'
Configuration: minimap2 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)	11,066 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 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 'minimap2 Myco', column 'Rate (reads/s)*'
Configuration: minimap2 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)	0.996 recall fraction · higher Uncertainty: 95% CI 0.9954 to 0.9955. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 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 'minimap2 Myco', column 'Sensitivity (95% CI)'
Configuration: minimap2 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 0.9996 to 0.9997. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 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 'minimap2 Myco', column 'Specificity (95% CI)'
Configuration: minimap2 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)	0.995 youden-index fraction · higher Uncertainty: 95% CI 0.9951 to 0.9951. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 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 'minimap2 Myco', column 'Youden’s index (95% CI)'
Configuration: minimap2 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)	7.9 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 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 'minimap2 Myco', column 'Memory (GB)†'
Configuration: minimap2 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)	332 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 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 'minimap2 Myco', column 'Rate (reads/s)*'
Configuration: minimap2 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)	0.981 recall fraction · higher Uncertainty: 95% CI 0.9803 to 0.9819. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 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 'minimap2 Myco', column 'Sensitivity (95% CI)'
Configuration: minimap2 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 0.9995 to 0.9995. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 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 'minimap2 Myco', column 'Specificity (95% CI)'
Configuration: minimap2 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)	0.981 youden-index fraction · higher Uncertainty: 95% CI 0.9797 to 0.9815. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 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 'minimap2 Myco', column 'Youden’s index (95% CI)'
Configuration: minimap2 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)	11 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 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 'minimap2 Myco', column 'Memory (GB)†'
Configuration: minimap2 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)	49,727 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 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 'minimap2 Myco', column 'Rate (reads/s)*'
Configuration: minimap2 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 recall 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 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 'minimap2 Myco', column 'Sensitivity (95% CI)'
Configuration: minimap2 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 minimap2 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 'minimap2 Myco', column 'Specificity (95% CI)'
Configuration: minimap2 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 youden-index fraction · higher Uncertainty: 95% CI 0.9994 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 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 'minimap2 Myco', column 'Youden’s index (95% CI)'
Configuration: minimap2 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)	7.9 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 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 'minimap2 Myco', column 'Memory (GB)†'
Configuration: minimap2 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)	368 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 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 'minimap2 Myco', column 'Rate (reads/s)*'
Configuration: minimap2 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 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 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 'minimap2 Myco', column 'Sensitivity (95% CI)'
Configuration: minimap2 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 0.9997 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 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 'minimap2 Myco', column 'Specificity (95% CI)'
Configuration: minimap2 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 youden-index fraction · higher Uncertainty: 95% CI 0.9996 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 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 'minimap2 Myco', column 'Youden’s index (95% CI)'