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minimap2 MTB (Hall and Coin 2024)

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

Overview

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

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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-mtb

areas: microbes-communities
contexts: clinical_research
method types: conventional_pipeline
reported name: minimap2 MTB
source locator: Methods 'Mycobacterium read classification' paragraphs 2-3
foundation model eligible: false
parameters: Authors' database: M. tuberculosis H37Rv plus 17 high-quality M. tuberculosis genomes from lineages 1-6; -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 MTB (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)	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 MTB 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 MTB', column 'Memory (GB)†'
Configuration: minimap2 MTB (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)	82,194 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 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 MTB', column 'Rate (reads/s)*'
Configuration: minimap2 MTB (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)	0.942 recall fraction · higher Uncertainty: 95% CI 0.9415 to 0.9417. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 MTB 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 MTB', column 'Sensitivity (95% CI)'
Configuration: minimap2 MTB (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)	0.988 specificity fraction · higher Uncertainty: 95% CI 0.9883 to 0.9884. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 MTB 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 MTB', column 'Specificity (95% CI)'
Configuration: minimap2 MTB (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)	0.93 youden-index fraction · higher Uncertainty: 95% CI 0.9298 to 0.9301. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 MTB 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 MTB', column 'Youden’s index (95% CI)'
Configuration: minimap2 MTB (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)	2.5 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 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 MTB', column 'Memory (GB)†'
Configuration: minimap2 MTB (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)	1,892 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 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 MTB', column 'Rate (reads/s)*'
Configuration: minimap2 MTB (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)	0.945 recall fraction · higher Uncertainty: 95% CI 0.9436 to 0.9464. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 MTB 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 MTB', column 'Sensitivity (95% CI)'
Configuration: minimap2 MTB (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)	0.982 specificity fraction · higher Uncertainty: 95% CI 0.9816 to 0.9821. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 MTB 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 MTB', column 'Specificity (95% CI)'
Configuration: minimap2 MTB (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)	0.927 youden-index fraction · higher Uncertainty: 95% CI 0.9252 to 0.9285. Wilson score interval (table footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source minimap2 MTB 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 MTB', 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)'
Configuration: minimap2 MTB (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)	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 MTB 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 MTB', column 'Memory (GB)†'
Configuration: minimap2 MTB (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)	418 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 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 MTB', column 'Rate (reads/s)*'
Configuration: minimap2 MTB (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)	0.97 recall fraction · higher Uncertainty: 95% CI 0.969 to 0.9717. 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 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 MTB', column 'Sensitivity (95% CI)'
Configuration: minimap2 MTB (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)	0.974 specificity fraction · higher Uncertainty: 95% CI 0.9715 to 0.9753. 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 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 MTB', column 'Specificity (95% CI)'
Configuration: minimap2 MTB (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)	0.944 youden-index fraction · higher Uncertainty: 95% CI 0.9405 to 0.9469. 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 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 MTB', column 'Youden’s index (95% CI)'